A plant genus of the family ARACEAE. The name derived from ar (fire in Arabic) due to the irritating sap. Flower is a spathe.
Sequential operating programs and data which instruct the functioning of a digital computer.
The portion of an interactive computer program that issues messages to and receives commands from a user.
The relationships of groups of organisms as reflected by their genetic makeup.
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
Databases devoted to knowledge about specific genes and gene products.
Family of large marine CRUSTACEA, in the order DECAPODA. These are called clawed lobsters because they bear pincers on the first three pairs of legs. The American lobster and Cape lobster in the genus Homarus are commonly used for food.
Software designed to store, manipulate, manage, and control data for specific uses.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Loss of functional activity and trophic degeneration of nerve axons and their terminal arborizations following the destruction of their cells of origin or interruption of their continuity with these cells. The pathology is characteristic of neurodegenerative diseases. Often the process of nerve degeneration is studied in research on neuroanatomical localization and correlation of the neurophysiology of neural pathways.
A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
Systematic organization, storage, retrieval, and dissemination of specialized information, especially of a scientific or technical nature (From ALA Glossary of Library and Information Science, 1983). It often involves authenticating or validating information.
A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.
Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
The systematic study of the complete DNA sequences (GENOME) of organisms.
Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.
Organized activities related to the storage, location, search, and retrieval of information.
A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.
Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Functions constructed from a statistical model and a set of observed data which give the probability of that data for various values of the unknown model parameters. Those parameter values that maximize the probability are the maximum likelihood estimates of the parameters.
A stochastic process such that the conditional probability distribution for a state at any future instant, given the present state, is unaffected by any additional knowledge of the past history of the system.
Remains, impressions, or traces of animals or plants of past geological times which have been preserved in the earth's crust.
A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.
Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)
A specified list of terms with a fixed and unalterable meaning, and from which a selection is made when CATALOGING; ABSTRACTING AND INDEXING; or searching BOOKS; JOURNALS AS TOPIC; and other documents. The control is intended to avoid the scattering of related subjects under different headings (SUBJECT HEADINGS). The list may be altered or extended only by the publisher or issuing agency. (From Harrod's Librarians' Glossary, 7th ed, p163)
Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.
Computer-based representation of physical systems and phenomena such as chemical processes.
Genotypic differences observed among individuals in a population.
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
The genetic complement of a BACTERIA as represented in its DNA.
Computer processing of a language with rules that reflect and describe current usage rather than prescribed usage.
Use of sophisticated analysis tools to sort through, organize, examine, and combine large sets of information.
The terms, expressions, designations, or symbols used in a particular science, discipline, or specialized subject area.
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.
The genetic complement of a plant (PLANTS) as represented in its DNA.
The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
The protein complement of an organism coded for by its genome.
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
Sets of structured vocabularies used for describing and categorizing genes, and gene products by their molecular function, involvement in biological processes, and cellular location. These vocabularies and their associations to genes and gene products (Gene Ontology annotations) are generated and curated by the Gene Ontology Consortium.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
Any method used for determining the location of and relative distances between genes on a chromosome.
Specific languages used to prepare computer programs.
Theory and development of COMPUTER SYSTEMS which perform tasks that normally require human intelligence. Such tasks may include speech recognition, LEARNING; VISUAL PERCEPTION; MATHEMATICAL COMPUTING; reasoning, PROBLEM SOLVING, DECISION-MAKING, and translation of language.
The systematic study of the complete complement of proteins (PROTEOME) of organisms.
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
Infection with the Omsk hemorrhagic fever virus, a Flavivirus.
The complete gene complement contained in a set of chromosomes in a fungus.
The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.
Collections of facts, assumptions, beliefs, and heuristics that are used in combination with databases to achieve desired results, such as a diagnosis, an interpretation, or a solution to a problem (From McGraw Hill Dictionary of Scientific and Technical Terms, 6th ed).
Software used to locate data or information stored in machine-readable form locally or at a distance such as an INTERNET site.
In INFORMATION RETRIEVAL, machine-sensing or identification of visible patterns (shapes, forms, and configurations). (Harrod's Librarians' Glossary, 7th ed)
The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.
The relationships between symbols and their meanings.
A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).
A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.
Activities performed to identify concepts and aspects of published information and research reports.
Specifications and instructions applied to the software.
A bibliographic database that includes MEDLINE as its primary subset. It is produced by the National Center for Biotechnology Information (NCBI), part of the NATIONAL LIBRARY OF MEDICINE. PubMed, which is searchable through NLM's Web site, also includes access to additional citations to selected life sciences journals not in MEDLINE, and links to other resources such as the full-text of articles at participating publishers' Web sites, NCBI's molecular biology databases, and PubMed Central.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.
Biological molecules that possess catalytic activity. They may occur naturally or be synthetically created. Enzymes are usually proteins, however CATALYTIC RNA and CATALYTIC DNA molecules have also been identified.
Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.
Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
The complete genetic complement contained in a set of CHROMOSOMES in a protozoan.
A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.
Controlled operation of an apparatus, process, or system by mechanical or electronic devices that take the place of human organs of observation, effort, and decision. (From Webster's Collegiate Dictionary, 1993)
The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.
Biological activities and function of the whole organism in human, animal, microorgansims, and plants, and of the biosphere.
The functional hereditary units of PLANTS.
The continuous developmental process of a culture from simple to complex forms and from homogeneous to heterogeneous qualities.
A phenolphthalein that is used as a diagnostic aid in hepatic function determination.
A definite pathologic process with a characteristic set of signs and symptoms. It may affect the whole body or any of its parts, and its etiology, pathology, and prognosis may be known or unknown.
The genetic complement of a helminth (HELMINTHS) as represented in its DNA.
Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.
Application of statistical procedures to analyze specific observed or assumed facts from a particular study.
The premier bibliographic database of the NATIONAL LIBRARY OF MEDICINE. MEDLINE® (MEDLARS Online) is the primary subset of PUBMED and can be searched on NLM's Web site in PubMed or the NLM Gateway. MEDLINE references are indexed with MEDICAL SUBJECT HEADINGS (MeSH).
Text editing and storage functions using computer software.
The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.
Social media model for enabling public involvement and recruitment in participation. Use of social media to collect feedback and recruit volunteer subjects.
Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations.
The degree of 3-dimensional shape similarity between proteins. It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
Computerized compilations of information units (text, sound, graphics, and/or video) interconnected by logical nonlinear linkages that enable users to follow optimal paths through the material and also the systems used to create and display this information. (From Thesaurus of ERIC Descriptors, 1994)
The genetic complement of an insect (INSECTS) as represented in its DNA.
The genomic analysis of assemblages of organisms.
A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.
Structured vocabularies describing concepts from the fields of biology and relationships between concepts.
Systems where the input data enter the computer directly from the point of origin (usually a terminal or workstation) and/or in which output data are transmitted directly to that terminal point of origin. (Sippl, Computer Dictionary, 4th ed)
Description of pattern of recurrent functions or procedures frequently found in organizational processes, such as notification, decision, and action.
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Graphs representing sets of measurable, non-covalent physical contacts with specific PROTEINS in living organisms or in cells.
The systematic arrangement of entities in any field into categories classes based on common characteristics such as properties, morphology, subject matter, etc.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.

Function annotation of an SBP-box gene in Arabidopsis based on analysis of co-expression networks and promoters. (1/2076)

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Structural characterisation of the natively unfolded enterocin EJ97. (2/2076)

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Phenotypic annotation of the mouse X chromosome. (3/2076)

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Research resource: Gonadotropin-releasing hormone receptor-mediated signaling network in LbetaT2 cells: a pathway-based web-accessible knowledgebase. (4/2076)

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Structure of the cytoplasmic segment of histidine kinase receptor QseC, a key player in bacterial virulence. (5/2076)

QseC is a histidine kinase (HK) receptor involved in quorum sensing, a mechanism by which bacteria respond to fluctuations in cell population. We conducted a structural study of the cytoplasmic domain of QseC (QseC-CD) using X-ray crystallography. The 2.5 A structure of the apo-enzyme revealed that the kinase domain of QseC retains the overall fold of the typical HK kinase domain. The construct that we used is inactive in the autokinase reaction and its inactivity is most likely caused by its atypical dimerization interface, as compared to that observed in the T.maritima HK cytoplasmic domain structure. Restoration of the activity may require that the entire dimerization domain be present in the protein construct. QseC, which plays an important role in bacterial pathogenesis, is a promising drug target and the structure of QseC-CD provides a platform for developing more potent inhibitors of pathogen virulence.  (+info)

Rational redesign of porcine pepsinogen containing an antimicrobial peptide. (6/2076)

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Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays. (7/2076)

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Annotating conserved and novel features of primate transcriptomes using sequencing. (8/2076)

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Once the MODs annotations have been integrated into our database, UniProt-GOA will provide the MOD with a file in the GAF2.0 format containing the entire set of GO annotations that match the taxon identifier(s) the MOD is responsible for as well as any additional annotations the MOD has created to other taxons. When importing the annotations back into their own database, the MOD can either note the updates made in this set from the changes in the date attached to each annotation (dates indicate when the last edit was made to the annotation) or they can carry out a full delete and reload of their GO annotation set. Any annotations that we cannot accept from the MOD, but which the MOD wants to keep can be appended to the supplied GAF by the MOD, e.g. annotations to non-coding RNAs, annotations using internal references that arent mapped to a GO_REF, IEA annotations, etc. UniProt-GOA will not store the annotations that are excluded, so it is up to the MOD to keep a record of these. If required, ...
BACKGROUND: As a major stored-product pest insect, Liposcelis entomophila has developed high levels of resistance to various insecticides in grain storage systems. However, the molecular mechanisms underlying resistance and environmental stress have not been characterized. To date, there is a lack of genomic information for this species. Therefore, studies aimed at profiling the L. entomophila transcriptome would provide a better understanding of the biological functions at the molecular levels.. METHODOLOGY/PRINCIPAL FINDINGS: We applied Illumina sequencing technology to sequence the transcriptome of L. entomophila. A total of 54,406,328 clean reads were obtained and that de novo assembled into 54,220 unigenes, with an average length of 571 bp. Through a similarity search, 33,404 (61.61%) unigenes were matched to known proteins in the NCBI non-redundant (Nr) protein database. These unigenes were further functionally annotated with gene ontology (GO), cluster of orthologous groups of proteins ...
Q1. If there are duplicate manual annotations from both the MOD and UniProt, how will that be handled? A1. The UniProt-GOA database can handle duplicate annotations that differ only in source, therefore we will display duplicate annotations. We will be supplying all annotations to the species indicated in the file, regardless of which group created the annotation, so it would be up to each group to decide which they want to keep. However, if annotations from other groups are retained, attribution of these annotations must stay as the original source. Q2. Some MODs update their databases on a nightly basis and would therefore like to have more frequent data releases. Is that possible? A2. The default for supplying annotation files to groups is once every two weeks. If any group would like their file more often, we are happy to consider this within reason. There are certain times of the week when it is not possible to generate files (including at weekends) due to scheduling conflicts with other ...
Recent advances in global gene expression measurement and the development of large- scale public repositories for storage of such data have made a wealth of information available to researchers. While one gene expression study may lack sufficient replicates to make statistically significant pronouncements, the combination of studies through meta-analysis can yield results with a much greater likelihood of accuracy. In order to combine multiple sets of data, one must first address the issue of cross-comparison between global gene expression platforms, as well as resolve the issue of repeated measures (multiple probes representing the same gene) within each platform. In this work, I present computational methods for probe reannotation and scoring and for redundant probe consolidation that together allow for greatly improved access to data for meta-analysis. I also present an example of the application of these methods, in the analysis of the gene expression regulated by estrogen across multiple ...
Annotation: Augments the information the viewer can immediately see about the data with notes, sources, or other useful information. Ive been looking for data labeling for computer vision data. Hire a Netguru team to help you implement Data Annotation solutions. You can compare the annotations and privilege levels across vCenter Server instances and host machines. An up to date and manually curated list of top data annotation companies from all over the world. Image annotation describes the classification of information that is of relevance to an image. Genome and genome annotation. The annotations automatically save for the loaded security next time that security is pulled up. Image annotation. Ngene empowers LabVIEW development environment with Machine Learning/Deep Learning tools. ai provides high-quality training and validation data to enable mobility companies to develop with confidence computer vision and machine learning models that reliably and safely power autonomous vehicles. ...
Hemarthria R. Br. is an important genus of perennial forage grasses that is widely used in subtropical and tropical regions. Hemarthria grasses have made remarkable contributions to the development of animal husbandry and agro-ecosystem maintenance; however, there is currently a lack of comprehensive genomic data available for these species. In this study, we used Illumina high-throughput deep sequencing to characterize of two agriculturally important Hemarthria materials, H. compressa Yaan and H. altissima 1110. Sequencing runs that used each of four normalized RNA samples from the leaves or roots of the two materials yielded more than 24 million high-quality reads. After de novo assembly, 137,142 and 77,150 unigenes were obtained for Yaan and 1110, respectively. In addition, a total of 86,731 Yawn and 48,645 1110 unigenes were successfully annotated. After consolidating the unigenes for both materials, 42,646 high-quality SNPs were identified in 10,880 unigenes and 10,888 SSRs were ...
The Gene Ontology project integrates data about the function of gene products across a diverse range of organisms, allowing the transfer of knowledge from model organisms to humans, and enabling computational analyses for interpretation of high-throughput experimental and clinical data. The core data structure is the annotation, an association between a gene product and a term from one of the three ontologies comprising the GO. Historically, it has not been possible to provide additional information about the context of a GO term, such as the target gene or the location of a molecular function. This has limited the specificity of knowledge that can be expressed by GO annotations. The GO Consortium has introduced annotation extensions that enable manually curated GO annotations to capture additional contextual details. Extensions represent effector-target relationships such as localization dependencies, substrates of protein modifiers and regulation targets of signaling pathways and transcription factors
Gene-list annotations are critical for researchers to explore the complex relationships between genes and functionalities. Currently, the annotations of a gene list are usually summarized by a table or a barplot. As such, potentially biologically important complexities such as one gene belonging to multiple annotation categories are difficult to extract. We have devised explicit and efficient visualization methods that provide intuitive methods for interrogating the intrinsic connections between biological categories and genes. We have constructed a data model and now present two novel methods in a Bioconductor package, GeneAnswers, to simultaneously visualize genes, concepts (a.k.a. annotation categories), and concept-gene connections (a.k.a. annotations): the Concept-and-Gene Network and the Concept-and-Gene Cross Tabulation. These methods have been tested and validated with microarray-derived gene lists. These new visualization methods can effectively present annotations using Gene Ontology,
AceView offers a comprehensive annotation of human and nematode genes reconstructed by co-alignment and clustering of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes, their functions, alternative variants, expression, regulation and interactions, in the hope to stimulate further validating experiments at the bench
The genome sequence of an organism is an information resource unlike any that biologists have previously had access to. But the value of the genome is only as good as its annotation. It is the annotation that bridges the gap from the sequence to the biology of the organism. The aim of high-quality annotation is to identify the key features of the genome - in particular, the genes and their products. The tools and resources for annotation are developing rapidly, and the scientific community is becoming increasingly reliant on this information for ail aspects of biological research.. ...
Genomic locations of UniProt/SwissProt annotations are labeled with a short name for the type of annotation (e.g. glyco, disulf bond, Signal peptide etc.). A click on them shows the full annotation and provides a link to the UniProt/SwissProt record for more details. TrEMBL annotations are always shown in light blue, except in the Signal Peptides, Extracellular Domains, Transmembrane Domains, and Cytoplamsic domains subtracks.. Mouse over a feature to see the full UniProt annotation comment. For variants, the mouse over will show the full name of the UniProt disease acronym. The subtracks for domains related to subcellular location are sorted from outside to inside of the cell: Signal peptide, extracellular, transmembrane, and cytoplasmic. In the UniProt Modifications track, lipoification sites are highlighted in dark blue, glycosylation sites in dark green, and phosphorylation in light green.. Duplicate annotations are removed as far as possible: if a TrEMBL annotation has the same ...
Genomic locations of UniProt/SwissProt annotations are labeled with a short name for the type of annotation (e.g. glyco, disulf bond, Signal peptide etc.). A click on them shows the full annotation and provides a link to the UniProt/SwissProt record for more details. TrEMBL annotations are always shown in light blue, except in the Signal Peptides, Extracellular Domains, Transmembrane Domains, and Cytoplamsic domains subtracks.. Mouse over a feature to see the full UniProt annotation comment. For variants, the mouse over will show the full name of the UniProt disease acronym. The subtracks for domains related to subcellular location are sorted from outside to inside of the cell: Signal peptide, extracellular, transmembrane, and cytoplasmic. In the UniProt Modifications track, lipoification sites are highlighted in dark blue, glycosylation sites in dark green, and phosphorylation in light green.. Duplicate annotations are removed as far as possible: if a TrEMBL annotation has the same ...
Function ,p>Position-independent general annotations used to be found in the General annotation (Comments) section in the previous version of the UniProtKB entry view. They provide any useful information about the protein, mostly biological knowledge. General annotations are frequently written in free text, although we increasingly try to standardize them and use controlled vocabulary wherever possible. The flat file and XML formats still group all general annotation together in a Comments section (CC, ,comment>). ,p>,a href=/help/general_annotation target=_top>More...,/a>,/p>[CC]i ...
Function ,p>Position-independent general annotations used to be found in the General annotation (Comments) section in the previous version of the UniProtKB entry view. They provide any useful information about the protein, mostly biological knowledge. General annotations are frequently written in free text, although we increasingly try to standardize them and use controlled vocabulary wherever possible. The flat file and XML formats still group all general annotation together in a Comments section (CC, ,comment>). ,p>,a href=/help/general_annotation target=_top>More...,/a>,/p>[CC]i ...
Function ,p>Position-independent general annotations used to be found in the General annotation (Comments) section in the previous version of the UniProtKB entry view. They provide any useful information about the protein, mostly biological knowledge. General annotations are frequently written in free text, although we increasingly try to standardize them and use controlled vocabulary wherever possible. The flat file and XML formats still group all general annotation together in a Comments section (CC, ,comment>). ,p>,a href=/help/general_annotation target=_top>More...,/a>,/p>[CC]i ...
Motivation Function annotations of gene products, and phenotype annotations of genotypes, provide valuable information about molecular mechanisms that can be utilized by computational methods to identify functional and phenotypic relatedness, improve our understanding of disease and pathobiology, and lead to discovery of drug targets. Identifying functions and phenotypes commonly requires experiments which are time-consuming and expensive to carry out; creating the annotations additionally requires a curator to make an assertion based on reported evidence. Support to validate the mutual consistency of functional and phenotype annotations as well as a computational method to predict phenotypes from function annotations, would greatly improve the utility of function annotations. Results We developed a novel ontology-based method to validate the mutual consistency of function and phenotype annotations. We apply our method to mouse and human annotations, and identify several inconsistencies that can ...
The Distributed Annotation System, or DAS, is a protocol for exchanging and retrieving sequence annotations, possibly from multiple sources. With DAS you dont have to store annotation data to use or display it. You only have to know how to retrieve it from a DAS server. See the BioDas web site for a full explanation of DAS ...
GO annotations: Mouse from MGI; Human from GO Annotations @ EBI (GOA); Rat from RGD; Chicken from GOA; Fly from FlyBase; Pfalc from PlasmoDB; Worm from WormBase; Dicty from dictyBase; Yeast from SGD; Zfin from ZFIN; Tair from TAIR/TIGR; Rice from Gramene; Pombe from Sanger GeneDB ...
We have set up the Gene Search page, users can submit gene locus, GO or InterPro category, or functional information, the server will return detailed gene annotation, including predicted functional information, homologs in Arabidopsis thaliana and Oryza sativa, domain assignment, GO and Mapman annotation, etc.. ...
Ab initio annotation of sequences in Human genome draft: (49171 Genes and 282378 exons) The nucleotide sequence of nearly 90% of the Human genome (3 GB) has been determined in worldwide sequencing community. We annotated these sequences predicting genes by one of the most accurate FGENESH program (at http://www.softberry.com/nucleo.html) and annotated similarity of each exon with the PfamA protein domain database. The complete results of this analysis are presented in Table 1 and can be seen in the InfoGene database at: http://www.softberry.com/inf/infodb.html where the Infogen Java viewer can by used to visualize the predictions along the chromosomes and by Action meny and Obtain Locus to get Prediction data Blast search against the predicted Human proteins is provided at: httpd: //www.softberry.com/scan.html . The sequences of exons and gene annotation data can be copied for using them locally or to create microarray oligos: ,Human genome predicted genes/exons ,Predicted amino acid sequences ...
The definition of a protein coding domain that we used here is a contiguous stretch of DNA that, when transcribed, produces an mRNA that specifies the amino acid sequence of a protein. The T7 protein coding domains were first characterized by the isolation and analysis of randomly generated amber mutants. Nineteen genes were identified by mapping mutants that disrupt T7 DNA synthesis, particle maturation, and lysis (Studier, 1969; Haussman & Gomez, 1967; Haussman & LaRue, 1969). Two additional genes, T7 DNA ligase and protein kinase, were isolated via loss of function and deletion, respectively (Masamune et al, 1971); the genetic analysis of ligase and kinase mutants was carried out using mutant host strains that do not support the growth of ligase or kinase defective phage (Studier, 1969). Up to thirty T7 proteins were observed by pulsing phage-infected cells with radioactive amino acids (Studier & Maizel, 1969; Studier, 1973). Further experiments, such as electrophoretic mobility shifts of ...
FatiGO is a web-accessible application that functions in much the same way as DAVIDs GoCharts, including the ability to specify term-specificity level. Unlike DAVID, FatiGO does not allow the setting of a minimum hit threshold for simplified viewing of only the most highly represented functional categories. Likewise, FatiGO limits the graphical output to only one top-level GO category at a time, whereas DAVID allows the combined viewing of biological process, molecular function, and cellular component annotations simultaneously. FatiGOs static barchart output looks very similar to DAVIDs GoChart; an important distinction is that DAVIDs GoCharts are dynamic, allowing users to drill-down and traverse the GO hierarchy for any subset of genes, view the underlying chart data and associated annotations, and link out to external data repositories including LocusLink and QuickGO. As shown in Table 3 the majority of accession types accepted and functional annotations offered by DAVID are not ...
PacBio calls their technology SMRT sequencing - single molecule, real-time. Unlike most other sequencing technologies, it doesnt require clonal amplification of DNA - it sequences single molecules. The real-time nature of PacBio leads to three distinct advantages. First, the reads are quite fast, with runs lasting from 30 minutes to three hours (rather than days). Second, the reads are substantially longer than most other commercially available sequencing platforms (including Sanger-based sequencers), with a mean of ~15 kb. Third, the movie captures information about the rate of nucleotide incorporation, which can be used to determine the modification status of the template nucleotide (e.g. 5-mC, 5-hmC, etc.). The raw read error rate is substantially higher at around 14% compared with the 0.1 to 1% error rate of other leading systems. However, unlike the others, the error model is stochastic, so very high quality reads across all bases can be achieved in the consensus sequence. Additionally, ...
Methods, systems, and articles of manufacture that may be used to create and share annotations for query components, such as query conditions, in an effort to share domain knowledge, are provided. The annotations may be created by users with particular domain knowledge and may contain information useful to other users when building queries including the annotated query components. An annotation may indicate a particular format or syntax for an associated query component. In some cases, a replacement to the associated query component is suggested.
Why does the choice of a gene model have so dramatic an effect on gene quantification? Below, we chose a few extreme or representative cases to provide possible explanations. In the liver sample, the expression levels for these exemplary genes for both Ensembl and RefGene were summarized in Table 2 (read length = 75 bp). PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha) uses ATP to phosphorylate PtdIns, PtdIns4P, and PtdIns(4,5)P2. In the liver sample, there were 1094 reads mapped to PIK3CA in Ensembl annotation, while only 492 reads were mapped in RefGene. The PIK3CA gene definition in both Ensembl and RefGene, and the mapping profile of RNA-Seq reads were shown in Figure 6. Clearly, the difference in gene definition gives rise to the observed discrepancy in quantification ...
Dear Ernesto, our curation protocol found a mouse gene annotation in this pathway. There seems to be a human ortholog: ENSG00000020922 Can you let me know if the mouse gene is there deliberately or if they Ensembl identifier can be updated? Thanks, Egon ...
You may suggest updates to the annotation of this entry using this form. Suggestions will be sent to our curators for review and, if acceptable, will be included in the next public release of InterPro. It is helpful if you can include literature references supporting your annotation suggestion. ...
You may suggest updates to the annotation of this entry using this form. Suggestions will be sent to our curators for review and, if acceptable, will be included in the next public release of InterPro. It is helpful if you can include literature references supporting your annotation suggestion. ...
Author Summary Understanding gene function-how individual genes contribute to the biology of an organism at the molecular, cellular and organism levels-is one of the primary aims of biomedical research. It has been a longstanding tenet of model organism research that experimental knowledge obtained in one organism is often applicable to other organisms, particularly if the organisms share the relevant genes because they inherited them from their common ancestor. Nevertheless this tenet is, like any hypothesis, not beyond question. A recent paper has termed this hypothesis a
In metagenomics datasets, it is standard practice to correct samples for (a) differences in sequencing effort (library size) and (b) normalise gene counts based on the total annotated hits per sample to obtain relative abundances. However, most databases on functional genes such as SEED or KEGG are biased, such that genes involved in central metabolism are better annotated. Hence, categories such as Carbohydrate metabolism and protein synthesis often dominate function profiles as result of this bias. Most articles do not correct for this database bias. What are the common ways of accounting for this bias?. ...
geneid - Gene prediction tool, it can also introduce homology and annotation evidences and produce a reannotation of a genomic sequence. A pthreads parallel version also available ...
Function ,p>Position-independent general annotations used to be found in the General annotation (Comments) section in the previous version of the UniProtKB entry view. They provide any useful information about the protein, mostly biological knowledge. General annotations are frequently written in free text, although we increasingly try to standardize them and use controlled vocabulary wherever possible. The flat file and XML formats still group all general annotation together in a Comments section (CC, ,comment>). ,p>,a href=/help/general_annotation target=_top>More...,/a>,/p>[CC]i ...
protein orthologs and functional annotation meta-server ORCAN is a web app that performs a real time orthologous sequence detection and facilitate evolutionary and functional annotation of a protein of interest.. ORCAN intergrates: 4 orthology detection programs, 5 on-line orthology databases and 5 sequence annotation tools using the most up to date reference data sets.. ...
Has no ubiquitin ligase activity on its own. TheUBE2V2/UBE2N heterodimer catalyzes the synthesis of non-canonicalpoly-ubiquitin chains that are linked through Lys-63. This typeof poly-ubiquitination does not lead to protein degradation by theproteasome. Mediates transcriptional activation of target genes.Plays a role in the control of progress through the cell cycle anddifferentiation. Plays a role in the error-free DNA repair pathwayand contributes to the survival of cells after DNA damage.{ECO:0000269,PubMed:10089880, ECO:0000269,PubMed:14562038,ECO:0000269,PubMed:20061386, ECO:0000269,PubMed:9705497 ...
Nitraria sibirica Pall., a typical halophyte of great ecological value, is widely distributed in desert, saline, and coastal saline-alkali environments. Consequently, researching the salt tolerance mechanism of N. sibirica Pall. has great significance to the cultivation and utilization of salt-tolerant plants. In this research, RNA-seq, digital gene expression (DGE), and high flux element analysis technologies were used to investigate the molecular and physiological mechanisms related to salt tolerance of N. sibirica Pall. Integrative analysis and de novo transcriptome assembly generated 137,421 unigenes. In total, 58,340 and 34,033 unigenes were annotated with gene ontology (GO) terms and mapped in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. Three differentially expressed genes (DEGs) libraries were subsequently constructed from the leaves of N. sibirica Pall. seedlings under different treatments: control (CK), light short-term salt stress (CL2), and heavy long-term salt
The Ensembl human gene annotations have been updated using Ensembls automatic annotation pipeline. The updated annotation incorporates new protein and cDNA sequences which have become publicly available since the last GRCh37 genebuild (March 2009).. In release 67 (May 2012), we continue to display a joint gene set based on the merge between the automatic annotation from Ensembl and the manually curated annotation from Havana. This refined gene set corresponds to GENCODE release 12. The Consensus Coding Sequence (CCDS) identifiers have also been mapped to the annotations. More information about the CCDS project. Updated manual annotation from Havana is merged into the Ensembl annotation every release. Transcripts from the two annotation sources are merged if they share the same internal exon-intron boundaries (i.e. have identical splicing pattern) with slight differences in the terminal exons allowed. Importantly, all Havana transcripts are included in the final Ensembl/Havana merged (GENCODE) ...
Functional annotation of genomes is a critical aspect of the genomics enterprise. Without reliable assignment of gene function at the appropriate level of specificity, new genome sequences are plainly useless. The primary methodology used for genome annotation is the sequence database search, the results of which allow transfer of functional information from experimentally characterized genes (proteins) to their uncharacterized homologs in newly sequenced genomes [1,2,3]. However, general-purpose, archival sequence databases are not particularly suited for the purpose of genome annotation. The quality of the annotation of a new genome produced using a particular database critically depends on the reliability and completeness of the annotations in the database itself. As far as annotation is concerned, the purpose of primary sequence databases is to faithfully preserve the description attached to each sequence by its submitter. In their capacity as sequence archives, such databases include no ...
To the best of our knowledge, this is first study to address the variation of human-annotated 3D facial landmarks. Understanding the variation of manual annotations is important as components of registration, recognition, and machine learning are influenced by manual annotation errors. However, the current literature is sparse in area pertaining to 3D facial morphology and variation. We expect that an increase in the availability, accuracy, user friendliness (i.e. fewer operator demands) of 3D imaging scanners will probe the use of shape models in clinical diagnostics, as seen for example in orthopedic surgery [24]. However, to assess the putative clinical impact of such tools, it is important to understand the variability embedded in manual annotation. Our analysis focused on facial morphology, suggests a procedure to retrieve a dense correspondence mesh of the face with low variance and minimal human operator assigned annotation points.. We first address the variability of 73 facial 3D ...
How will this virtual institute work? It will be divided into nodes, each focused on one aspect of genome annotation. The annotations generated will be integrated and made freely accessible to all through a single portal on the web, and will be used as a means of guiding future experimental work. Experimental validation of a statistically significant subset of computational predictions will be an integral part of the process, leading to an iterative improvement in methods, explains Thornton. The annotations will be integrated using DAS (Distributed Annotation System), an Open Source system developed by researcher Lincoln Stein and colleagues at Cold Spring Harbor Laboratory (NY, USA) for exchanging annotations on genomic sequence data. DAS heralds a new era for database structure, where information is distributed by a network rather than a single site, explains Søren Brunak. Meetings and workshops organized by the institute will encourage cooperation and reduce duplication of effort. They ...
Abstract Background While studies of non-model organisms are critical for many research areas, such as evolution, development, and environmental biology, they present particular challenges for both experimental and computational genomic level research. Resources such as mass-produced microarrays and the computational tools linking these data to functional annotation at the system and pathway level are rarely available for non-model species. This type of systems-level analysis is critical to the understanding of patterns of gene expression that underlie biological processes. Results We describe a bioinformatics pipeline known as FunnyBase that has been used to store, annotate, and analyze 40,363 expressed sequence tags (ESTs) from the heart and liver of the fish, Fundulus heteroclitus. Primary annotations based on sequence similarity are linked to networks of systematic annotation in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and can be queried and computationally ...
Upon the completion of whole genome sequencing, thorough genome annotation that associates genome sequences with biological meanings is essential. Genome annotation depends on the availability of transcript information as well as orthology information. In teleost fish, genome annotation is seriously hindered by genome duplication. Because of gene duplications, one cannot establish orthologies simply by homology comparisons. Rather intense phylogenetic analysis or structural analysis of orthologies is required for the identification of genes. To conduct phylogenetic analysis and orthology analysis, full-length transcripts are essential. Generation of large numbers of full-length transcripts using traditional transcript sequencing is very difficult and extremely costly. In this work, we took advantage of a doubled haploid catfish, which has two sets of identical chromosomes and in theory there should be no allelic variations. As such, transcript sequences generated from next-generation sequencing can be
Background Distinguishing between individuals is critical to those conducting animal/plant breeding, food safety/quality research, diagnostic and clinical testing, and evolutionary biology studies. Classical genetic identification studies are based on marker polymorphisms, but polymorphism-based techniques are time and labor intensive and often cannot distinguish between closely related individuals. Illumina sequencing technologies provide the detailed sequence data required for rapid and efficient differentiation of related species, lines/cultivars, and individuals in a cost-effective manner. Here we describe the use of Illumina high-throughput exome sequencing, coupled with SNP mapping, as a rapid means of distinguishing between related cultivars of the lignocellulosic bioenergy crop giant miscanthus (Miscanthus × giganteus). We provide the first exome sequence database for Miscanthus species complete with Gene Ontology (GO) functional annotations. Results A SNP comparative analysis of rhizome
ISSUE-72 (Annotation Semantics): REPORTED: lack of annotation semantics is not backwardly compatible http://www.w3.org/2007/OWL/tracker/issues/ Raised by: Jeremy Carroll On product: The semantics doc explicitly gives no semantics to annotations. This is not backwardly compatible with OWL 1.0 in which annotations have the RDFS semantics ...
We would like to get your feedback about GenDB. Please take a few seconds to fill out our survey.. GenDB is a genome annotation system for prokaryotic genomes. The system has been developed as an extensible and user friendly framework for both bioinformatics researchers and biologists to use in their genome projects. The GenDB annotation engine will automatically identify, classify and annotate genes using a large collection of software tools. Many groups view this automatic annotation as the first step that needs to be followed by expert annotation of the genome.. GenDB offers user interfaces that allow expert annotation with large, geo-graphically dispersed teams of experts. Genes to be annotated can be categorized by functional class or gene location. A number of naming schemes (aka ontologies or functional classification schemes) are supported: EC numbers, GO, COG. In addition to its use as a production genome annotation system, it can be employed as a flexible framework for the large-scale ...
I previously created a C.bairdi de novo transcriptome assembly v4.0 with Trinity from all our C.bairdi RNAseq reads which had BLASTx matches to the C.opilio genome and decided to assess its
The ever-increasing number of sequenced and annotated genomes has made management of their annotations a significant undertaking, especially for large eukaryotic genomes containing many thousands of genes. Typically, changes in gene and transcript numbers are used to summarize changes from release to release, but these measures say nothing about changes to individual annotations, nor do they provide any means to identify annotations in need of manual review. In response, we have developed a suite of quantitative measures to better characterize changes to a genomes annotations between releases, and to prioritize problematic annotations for manual review. We have applied these measures to the annotations of five eukaryotic genomes over multiple releases - H. sapiens, M. musculus, D. melanogaster, A. gambiae, and C. elegans. Our results provide the first detailed, historical overview of how these genomes annotations have changed over the years, and demonstrate the usefulness of these measures for genome
WebApollo is a browser-based tool for visualization and editing of sequence annotations. It is designed for distributed community annotation efforts, where numerous people may be working on the same sequences in geographically different locations; real-time updating keeps all users in sync during the editing process. The features of WebApollo include: *History tracking, including browsing of an annotations edit history and full undo/redo functions *Real time updating: edits in one client are instantly pushed to all other clients *Convenient management of user login, authentication, and edit permissions *Two-stage curation process: edit within a temporary workspace, then publish to a curated database *Ability to add comments, either chosen from a pre-defined set of comments or as freeform text. *Ability to add dbxrefs [database crossreferences] -- e.g. for GO functional annotation *Can set start of translation for a transcript or let server determine automatically *Flagging of non-canonical ...
Citation. Florea, L., Di Francesco, V., Miller, J., Turner, R., Yao, A., Harris, M., Walenz, B., Mobarry, C., Merkulov, G. V., Charlab, R., Dew, I., Deng, Z., Istrail, S., Li, P., Sutton, G.. Gene and Alternative Splicing Annotation With AIR. Genome Res. 2005 Jan 01; 15(1). : 54-66.. PubMed Citation. Abstract. Designing effective and accurate tools for identifying the functional and structural elements in a genome remains at the frontier of genome annotation owing to incompleteness and inaccuracy of the data, limitations in the computational models, and shifting paradigms in genomics, such as alternative splicing. We present a methodology for the automated annotation of genes and their alternatively spliced mRNA transcripts based on existing cDNA and protein sequence evidence from the same species or projected from a related species using syntenic mapping information. At the core of the method is the splice graph, a compact representation of a gene, its exons, introns, and alternatively spliced ...
Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at download page. ...
We performed a comparative analysis of five regulatory annotations, all based on diverse epigenomic signatures, to better understand their regulatory capacity and downstream transcriptional effects. We observed that stretch, super, and typical enhancers overlap enhancer chromatin states in the corresponding cell type, but overlap nonenhancer chromatin states in unrelated cell types, supporting the cell type specificity of these regulatory elements. These observations highlight H3K27ac as a good proxy for cell type-specific regulatory function. Annotations based on the H3K4me3 mark (broad domains) and TF binding (HOT regions) show a large fraction (,40%) of overlaps with promoter chromatin states across different cell types. Consistent with our observations, a recent study in the fly reported that regions bound by large numbers of TFs (such as HOT regions) are less cell type-specific (Kudron et al. 2017). While the diverse ChIP-seq data used to define regulatory annotations comes from different ...
Hi all, I used spades for assembly of bacteria-Illumina reads, and galaxy-Prokka for annotation Visualization of the annotation results showed me:. Summary of the active entries: contigs: 65. bases: 5736331. CDS: 5102. gene: 5279. misc_RNA: 52. rRNA: 9. tRNA: 115. tmRNA: 1. 1- how can I confirm that annotation results are correct? 2- I am confused, why there are no pseudogenes in my report!! Thanks for your time ...
But, by resorting to computational annotation of the function of proteins, we need to know how well can these algorithms actually perform. Enter CAFA, of which I have written before. CAFA is a community challenge that assesses the performance of protein function prediction algorithms.. How does the CAFA challenge work? Well, briefly:. 1. Target selection: we select a large number of proteins from SwissProt, UniProt-GOA and other databases. Those proteins have no experimental annotations, only computational ones. Those are the prediction targets.. 2. Prediction phase: we publish the targets. Participating CAFA teams now have four months to provide their own functional annotations, using the Gene Ontology, a controlled vocabulary describing protein functions.. 3. Growth phase: after four months, we close the predictions, and wait for another six months, or so. During those six months, some of the targets acquire experimentally-validated annotations. This typically means that biocurators have ...
Here is the first batch of annotations for The Alloy of Law. As with all of the other annotations here on the site, each annotation contains spoilers for the current chapter. Spoilers for chapters after the current one are hidden by spoiler tags. We recommend you read the book before reading the ...
Here is the first batch of annotations for The Alloy of Law. As with all of the other annotations here on the site, each annotation contains spoilers for the current chapter. Spoilers for chapters after the current one are hidden by spoiler tags. We recommend you read the book before reading the ...
Diagnosis Index entries containing back-references to J Toggle navigation. The following code s above J In this context, annotation back-references refer to codes that contain: Applicable To annotations, or Code Also annotations, or Code First annotations, or Excludes1 icd, or Excludes2 annotations, or Includes annotations, or Note annotations, or Use Additional annotations. Diseases of allergt respiratory system Note Allrrgy a respiratory condition is described as occurring in more than one site and is not specifically indexed, it should be classified to allergy lower anatomic site e. Type 2 Excludes certain conditions ifd in the perinatal period P04 - P96 certain infectious and parasitic diseases AB99 complications of pregnancy, childbirth and the puerperium OO9A congenital malformations, deformations and chromosomal abnormalities QQ99 endocrine, nutritional and metabolic diseases E00 - E88 injury, poisoning and certain other consequences of external causes ST88 neoplasms CD49 smoke inhalation ...
Centromeric alpha satellite (AS) is composed of highly identical higher-order DNA repetitive sequences, which make the standard assembly process impossible. Because of this the AS repeats were severely underrepresented in previous versions of the human genome assembly showing large centromeric gaps. The latest hg38 assembly (GCA_000001405.15) employed a novel method of approximate representation of these sequences using AS reference models to fill the gaps. Therefore, a lot more of assembled AS became available for genomic analysis. We used the PERCON program previously described by us to annotate various suprachromosomal families (SFs) of AS in the hg38 assembly and presented the results of our primary analysis as an easy-to-read track for the UCSC Genome Browser. The monomeric classes, characteristic of the five known SFs, were color-coded, which allowed quick visual assessment of AS composition in whole multi-megabase centromeres down to each individual AS monomer. Such comprehensive annotation of AS
In view of the draft state of the Chinese Hamster reference genome and the incomplete annotation of noncoding RNAs, an extended reference gene model was built to use in our differential expression and methylation analysis. The resulting annotation was contained 26,270 protein coding and 78,873 noncoding transcribed regions encoding for 80,973 transcripts, including 51,193 long noncoding RNAs (lncRNAs) or processed transcripts.. ...
Dear all, I need to know if there is a key of colours and shapes for the graphical representation of annotations in proteins. for instance, if I need to have a pictorial representation of a domain or transcript then is there a standardized way to do it? So far I have seen that domains are usually represented as ellipses or rectangles, and metal bindings as non-filled circles, while active sites are red-filled circles. I am particular interested in the next type of annotations: Domain, Signal, Transit, Propeptide, Peptide, Topological domain, Intramembrane, Transmenbrane for ranges of sequences, and Metal binding, Active site, Modified residue, Lipidation, Glycosilation for point positions. I appreciate any information on this matter. Cheers, Leyla García EMBL-EBI, Cambridge, UK ...
Background. DNA sequences are pivotal for a wide array of research in biology. Large sequence databases, like GenBank, provide an amazing resource to utilize DNA sequences for large scale analyses. However, many sequences on GenBank contain more than one gene or are portions of genomes, and inconsistencies in the way genes are annotated and the numerous synonyms a single gene may be listed under provide major challenges for extracting large numbers of subsequences for comparative analysis across taxa. At present, there is no easy way to extract portions from multiple GenBank accessions based on annotations where gene names may vary extensively. Results. The R package AnnotationBustR allows users to extract sequences based on GenBank annotations through the ACNUC retrieval system given search terms of gene synonyms and accession numbers. AnnotationBustR extracts portions of interest and then writes them to a FASTA file for users to employ in their research endeavors. Conclusion. FASTA files of extracted
Next-generation sequencing (NGS) is increasingly being applied across the drug discovery and development pathway e.g. in target evaluation, patient stratification and clinical profiling. However, biological interpretation of the output of NGS is highly time-consuming, being a mostly manual process of literature searching and annotation of the gene results. This webinar will show how I2E can be used to collate a comprehensive gene profile, with key biological annotation from a combination of sources like MEDLINE, OMIM and NIH Grants.
Sequence analysis (Figure 4): The sequenced PCR product generated 801 bases of high-quality reads that were used to identify the genus of the isolated colony. The chromatogram of the sequence is available as a pdf (14R_PREMIX_JF7523_18). The NCBI BLAST analysis revealed 99% identity with bases 50-850 of the 16s RNA gene of Bacillus aerius, Bacillus stratosphericus, and Bacillus altitudinis (Figure 4) ...
This tool converts genome coordinates and genome annotation files between assemblies. The input data can be pasted into the text box or uploaded from a file. For more information, please see our LiftOver documentation. If a pair of assemblies cannot be selected from the pull-down menus, a sequential lift may still be possible. For example, to lift from mm9 to mm39, lift from Mouse mm9 to mm10 and then from mm10 to mm39 ...
This tool converts genome coordinates and genome annotation files between assemblies. The input data can be pasted into the text box or uploaded from a file. For more information, please see our LiftOver documentation. If a pair of assemblies cannot be selected from the pull-down menus, a sequential lift may still be possible. For example, to lift from mm9 to mm39, lift from Mouse mm9 to mm10 and then from mm10 to mm39 ...
Cozzetto, Domenico; Jones, David T. (2017). "Computational Methods for Annotation Transfers from Sequence". In Dessimoz, C; ... molecular function, the elemental activities of a gene product at the molecular level, such as binding or catalysis; ... Annotation[edit]. Genome annotation encompasses the practice of capturing data about a gene product, and GO annotations use ... Annotations from automated processes (for example, remapping annotations created using another annotation vocabulary) are given ...
... public release of sequence data, assembly, annotation and publication strategies". Molecular Ecology Resources. 16 (1): 254-265 ... The advent of molecular techniques for phylogenetic analysis transformed understanding of oak relationships, initially by ... Frascaria, N.; Maggia, L.; Michaud, M.; Bousquet, J. (1993). "The RBCL Gene Sequence from Chestnut Indicates a Slow Rate of ... ISBN 0-19-509974-5. Conte, L.; Cotti, C.; Cristofolini, G. (2007). "Molecular evidence for hybrid origin of Quercus crenata Lam ...
These sequences are usually just molecular fossils, although they can occasionally serve as raw genetic material for the ... May 2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. Bibcode:2006Natur. ... The sequence on the opposite strand is called the "antisense" sequence. Both sense and antisense sequences can exist on ... The DNA sequence may be aligned with other DNA sequences to identify homologous sequences and locate the specific mutations ...
The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Research. 7 (4): 273-81. ... Klug A (October 1999). "Zinc finger peptides for the regulation of gene expression". Journal of Molecular Biology. 293 (2): 215 ... "SNP linked to Gene ZNF280D(geneID:54816) Via Contig Annotation". NCBI. Retrieved 10 May 2014. "Genomatix". Genomatix. Retrieved ... Nagase T, Kikuno R, Nakayama M, Hirosawa M, Ohara O (August 2000). "Prediction of the coding sequences of unidentified human ...
Strozzi F, Mazza R, Malinverni R, Williams JL (February 2009). "Annotation of 390 bovine miRNA genes by sequence similarity ... In molecular biology miR-181 microRNA precursor is a small non-coding RNA molecule. MicroRNAs (miRNAs) are transcribed as ~70 ... International Chicken Genome Sequencing Consortium (December 2004). "Sequence and comparative analysis of the chicken genome ... "Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of ...
... provides information on the resistant genes, their sequences, and their molecular functions. The database has over 700 ... 2013). "Gene Ontology annotations and resources". Nucleic Acids Research. 41 (Database issue) (Database issue): D530-D535. doi: ... The former's data is compiled from NCBI while the annotations are from UniProt and Gene Ontology. ... confirmed genes and over 150,000 predicted genes that are organized by molecular function and resistant phenotypes. As of 2019[ ...
Visualization of gene expression (heatmaps, volcano plot), molecular interaction networks (through Cytoscape), protein sequence ... and protein structure data (e.g., MarkUs). Integration of gene and pathway annotation information from curated sources as well ... sets and sequences. Dataset history tracking - complete record of data sets used and input settings. Integration with 3rd party ... sequence, and structure data. geWorkbench is the Bioinformatics platform of MAGNet, the National Center for the Multi-scale ...
"Sequence-based feature prediction and annotation of proteins". Genome Biology. 10 (2): 206. doi:10.1186/gb-2009-10-2-206. PMC ... He received his PhD in molecular biology in 1988 from the Autonomous University of Madrid. From 1989 to 1994 he was a ... 2011). "Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia". ... Valencia is Doctor Honoris cause of the Danish DTU and elected member of the European Molecular Biology Organization (EMBO). ...
The comparison of the sequences from these genes are sometimes used in molecular analysis to construct phylogenetic trees, for ... Several databases provide alignments and annotations of LSU rRNA sequences for comparative purposes: RDP, the Ribosomal ... Eperon, I. C.; Anderson, S.; Nierlich, D. P. (1980-07-31). "Distinctive sequence of human mitochondrial ribosomal RNA genes". ... Lafontaine, D. L. J.; Tollervey, D. (2001). "The function and synthesis of ribosomes". Nature Reviews Molecular Cell Biology. 2 ...
2005). "Generation and annotation of the DNA sequences of human chromosomes 2 and 4". Nature. 434 (7034): 724-31. doi:10.1038/ ... "Molecular & Cellular Proteomics. 11 (7): M111.011056. doi:10.1074/mcp.m111.011056. PMC 3394935. PMID 22375075.. ... Molecular function. • transferase activity. • transferase activity, transferring acyl groups other than amino-acyl groups. • ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ...
However, recent genome sequencing and annotation of S. endobioticum has shed light on the potential molecular mechanisms of ... Very little is known about the pathogenesis of S. endobioticum at a molecular level. Indeed, this is true of chytrids more ... The lack of hemicellulases may allow the pathogen to evade defense responses triggered by damage-associated molecular patterns ...
2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. Bibcode:2006Natur.441.. ... Chang WL, Lee DC, Leu S, Huang YM, Lu MC, Ouyang P (Aug 2003). "Molecular characterization of a novel nucleolar protein, pNO40 ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ...
... molecular biology and bioinformatics have created the need for DNA annotation. DNA annotation or genome annotation is the ... Improvements in DNA sequencing technology has meant that the cost of sequencing a new genome sequence has steadily fallen (in ... Rather than sequence a chromosome in one go, it would be sequenced piece by piece (with the prior knowledge of approximately ... The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism. For a bacterium ...
... and functional annotation of biological sequences. Karlowski graduated in molecular biology from the Faculty of Biology at the ... and evolutionary molecular biology analyses. Wojciech Karlowski is an expert in bioinformatics, molecular biology, molecular ... Sequence composition and genome organization of maize. Proc Natl Acad Sci U S A. 2004 Oct 5;101(40):14349-54. doi: 10.1073/pnas ... From 1991 to 1996 Karlowski continued his education in the area of plant molecular genetics in the frame of the Adam Mickiewicz ...
Further information: Sense (molecular biology). A DNA sequence is called a "sense" sequence if it is the same as that of a ... worth of DNA sequences, such as those produced by the Human Genome Project, are difficult to use without the annotations that ... The DNA sequence may be aligned with other DNA sequences to identify homologous sequences and locate the specific mutations ... the sequence of bases along a DNA strand defines a messenger RNA sequence, which then defines one or more protein sequences. ...
They include text mining, information management, sequence analysis, analysis of molecular interactions, and mathematical ... Allergome emphasizes the annotation of allergens that result in an IgE-mediated disease. A variety of computational, ... Methods that rely on sequence comparison are diverse and have been applied to analyze HLA sequence conservation, help verify ... improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap ...
2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. doi:10.1038/nature04727 ... Molecular and Cellular Biology portal. ... of more than 15,000 full-length human and mouse cDNA sequences ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ...
Following annotation, KEGG (Kyoto Encyclopedia of Genes and Genomes) enables visualization of metabolic pathways and molecular ... Blast2GO (B2G) enables Gene Ontology based data mining to annotate sequence data for which no GO annotation is available yet. ... Functional annotation of the assembled transcripts allows for insight into the particular molecular functions, cellular ... Whereas high sequence coverage for a genome may indicate the presence of repetitive sequences (and thus be masked), for a ...
It "simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features ... List of molecular graphics systems Molecular graphics List of software for molecular mechanics modeling Wang Y, Geer LY, ... Chappey C, Kans JA, Bryant SH (June 2000). "Cn3D: sequence and structure views for Entrez". Trends Biochem. Sci. 25 (6): 300-2 ...
... annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences". Virology Journal. 4 ... Molecular and Cellular Biology. 13 (12): 7476-7486. doi:10.1128/mcb.13.12.7476. PMC 364819. PMID 8246965. Huang ZM, Yen TS (May ... Molecular Biology Reports. 42 (12): 1603-1614. doi:10.1007/s11033-015-3928-0. PMID 26514143. Panjaworayan N, Payungporn S, ...
Genome Biol Solovyev V, Salamov A. (2011) Automatic Annotation of Microbial Genomes and Metagenomic Sequences. In Metagenomics ... easy-to-use desktop application for sequence analysis and molecular biology data management. Besides bioinformatics his ... He is interested in genome structural and functional annotation and applying it for rational design of biological systems. ... Solovyev V.V. (1993) Fractal graphical representation and analysis of DNA and Protein sequences. BioSystems, 30, 137-160. Moroz ...
2005). "Generation and annotation of the DNA sequences of human chromosomes 2 and 4". Nature. 434 (7034): 724-31. doi:10.1038/ ... Methods In Molecular Biology. 477. pp. 195-206. doi:10.1007/978-1-60327-517-0_15. ISBN 978-1-60327-218-6. PMID 19082948. ... "Entrez Gene: ribonucleotide reductase M2". Pavloff N, Rivard D, Masson S, Shen SH, Mes-Masson AM (1992). "Sequence analysis of ...
As the process keeps going down we're reaching the point where every genome that can be sequenced will be sequenced. Lisacek, F ... From 1988 onward it has been a collaborative project with the Data Library group of the European Molecular Biology Laboratory ... His most important contribution is the input of human knowledge by careful manual annotation in protein-related data. While ... A little while later he created ENZYME, a nomenclature database on enzymes as well as SeqAnalRef, a sequence analysis ...
Simplified Molecular Input Line Entry Specification). PharmGKB gives drug/compound and its annotation. Transcripts: This ... Since the 1980s, sequence information has become increasingly abundant; subsequently many laboratories realized this and began ... Annotation unification: Different data sources often offer annotations with heterogeneous naming system. Annotation unification ... unique wealth of combinatorial annotations of human genes. Annotation combinatory: Using GeneDecks, one can get a set of ...
2005). "Generation and annotation of the DNAD sequences of human chromosomes 2 and 4". Nature. 434 (7034): 724-31. Bibcode: ... Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2. Genome ... Family with sequence similarity 49 member A FAM98A: Family with sequence similarity 98 member A FAM136A: Family with sequence ... These are normally found only at the ends of a chromosome, but in chromosome 2 there are additional telomere sequences in the ...
May 2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. Bibcode:2006Natur. ... Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2. Genome ... family with sequence similarity 46, member B FAM46C: family with sequence similarity 46, member C FAM76A: family with sequence ... Family with sequence similarity 63, member A FAM78B: family with sequence similarity 78, member B FAM129A: family with sequence ...
... community-based annotation of biological databases through Wikipedia, for example, annotation of the Rfam database through ... As of 2012, he has been Head of Protein Sequence Resources at EMBL-EBI. Bateman has also been involved in promoting the use of ... part of the European Molecular Biology Laboratory (EMBL) in Cambridge, UK. He has led the development of the Pfam biological ... He has also been involved in the use of Wikipedia for community-based annotation of biological databases. Bateman received a ...
The software has been cited in thousands of scientific molecular biology publications and is one of several tools for systems ... which contains biological and chemical interactions and functional annotations created from millions of individually modeled ... Laboratory Corporation and Quest Diagnostics to develop a solution for scoring genetic variation for next generation sequencing ... "Best of Show Award Winners Named at the Fifteenth International Molecular Medicine Tri-Conference" (Press release). Cambridge ...
2007). "The MN1 oncoprotein activates transcription of the IGFBP5 promoter through a CACCC-rich consensus sequence". J. Mol. ... "A genome annotation-driven approach to cloning the human ORFeome". Genome Biol. 5 (10): R84. doi:10.1186/gb-2004-5-10-r84. PMC ... Molecular function. • molecular function. Cellular component. • cellular component. Biological process. • multicellular ...
Nucleotide sequences for more than 300,000 organisms with supporting bibliographic and biological annotation. ... "Evaluation of the GenBank, EzTaxon, and BIBI Services for Molecular Identification of Clinical Blood Culture Isolates That ... Bulk submissions of Expressed Sequence Tag (EST), Sequence-tagged site (STS), Genome Survey Sequence (GSS), and High-Throughput ... The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their ...
Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2.. ... 2004). "The sequence and analysis of duplication-rich human chromosome 16". Nature. 432 (7020): 988-94. doi:10.1038/nature03187 ... Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome ... Molecular Psychiatry. 20: 140-147. doi:10.1038/mp.2014.145. PMID 25421402.. ...
Gregory SG, Barlow KF, McLay KE (2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091 ... Molecular function. • G-protein coupled receptor activity. • olfactory receptor activity. • signal transducer activity. ...
2005). "Generation and annotation of the DNA sequences of human chromosomes 2 and 4". Nature. 434 (7034): 724-31. doi:10.1038/ ... Molecular function. • amyloid-beta binding. • signal transducer activity. • Wnt-protein binding. • protein binding. • protein ... Saitoh T, Hirai M, Katoh M (Jun 2001). "Molecular cloning and characterization of human Frizzled-5 gene on chromosome 2q33.3- ... "Purification and molecular cloning of a secreted, Frizzled-related antagonist of Wnt action". Proc. Natl. Acad. Sci. U.S.A. 94 ...
2005). "Generation and annotation of the DNA sequences of human chromosomes 2 and 4". Nature. 434 (7034): 724-31. Bibcode: ... Molecular function. • cyclin-dependent protein kinase 5 activator activity. • lipid binding. Cellular component. • cytoplasm. • ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A ...
"Molecular and. General Genetics. 165: 221. doi:10.1007/BF00269910.. *^ Strachan, Tom; Read, Andrew P. (1999). "Chromosome ... The 46/47 annotation indicates that the XY cells have the normal number of 46 total chromosomes, and the XXY cells have a total ... which are short sequences of DNA, and induces recombination between them. FRT sites have been inserted transgenically near the ... "Human Molecular Genetics (2nd ed.). New York: Wiley-Liss. ISBN 1-85996-202-5. PMID 21089233.. [page needed] ...
2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. PMID 16710414. doi: ... Eissmann P، Watzl C (2006). "Molecular analysis of NTB-A signaling: a role for EAT-2 in NTB-A-mediated activation of human NK ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A ...
... and brief annotations. The work, which included his own bio-bibliography, listed some three thousand authors alphabetically, ... "Molecular structure of Nucleic Acids". *Linus Pauling *"Sickle Cell Anemia, a Molecular Disease" ...
Molecular Phylogenetics and Evolution. 41 (2): 405-419. doi:10.1016/j.ympev.2006.05.039. PMID 16839785. Archived from the ... The nuclear,[50] mitochondrial[51][52] and chloroplast[53] genomes of British Columbia interior spruce have been sequenced. The ... genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism". The Plant ... "Picea glauca, whole genome shotgun sequencing project". 13 March 2015.. Cite journal requires ,journal=. (help). ...
Bernstein H, Hopf FA, Michod RE (1987). "The molecular basis of the evolution of sex". Molecular Genetics of Development. ... Most of the sequence pairs are greater than 99.97% identical. The extensive use of gene conversion may play a role in the ... Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome ... Strachan T, Read A (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2. .. ...
2006). "The DNA sequence and biological annotation of human chromosome 1". Nature 441 (7091): 315-21. doi:10.1038/nature04727. ... Wang J (2002). "Cellular roles of DNA topoisomerases: a molecular perspective". Nat Rev Mol Cell Biol 3 (6): 430-40. doi: ... 3.0 3.1 Alberts, Bruce; Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts and Peter Walters (2002). Molecular Biology ...
Proteopedia - Life in 3D: rotatable, zoomable 3D model with wiki annotations for every known protein molecular structure. ... The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In ... Methods in Molecular Biology (Clifton, N.j.). Methods in Molecular Biology. 815. pp. 15-24. doi:10.1007/978-1-61779-424-7_2. ... Methods in Molecular Biology. Methods in Molecular Biology™. 424. pp. 225-39. doi:10.1007/978-1-60327-064-9_19. ISBN 978-1- ...
Lesk, Arthur M. (2005). Database annotation in molecular biology. New York: John Wiley. ISBN 0-470-85681-5. .. ... Lesk, Arthur M. (1988). Computational molecular biology: sources and methods for sequence analysis. Oxford [Oxfordshire]: ... Arthur Mallay Lesk, is a protein science researcher, who is a professor of biochemistry and molecular biology at the ... He was a group leader in the biocomputing program at the European Molecular Biology Laboratory in Heidelberg, Germany, from ...
9] Sequences within ribosome binding site affecting messenger RNA translatability and method to direct ribosomes to single ... "Microbiology and Molecular Biology Reviews. 69 (1): 101-123. doi:10.1128/MMBR.69.1.101-123.2005. ISSN 1092-2172. PMC 1082788 . ... Gene annotation[edit]. The identification of RBSs is used to determine the site of translation initiation in an unannotated ... found within the Kozak consensus sequence ACCAUGG. Since the Kozak sequence itself is not involved in the recruitment of the ...
2006). "The DNA sequence and biological annotation of human chromosome 1.". Nature 441 (7091): 315-21. PMID 16710414. doi: ... Hamblin MW, Metcalf MA, McGuffin RW, Karpells S (1992). "Molecular cloning and functional characterization of a human 5-HT1B ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.". Proc. Natl. Acad. Sci. U.S.A ...
length of sequence. {\displaystyle (({\text{number of }}C+{\text{number of }}G)/2)^{2}/{\text{length of sequence}}}. [7]. Many ... the presence of a CpG island is used to help in the prediction and annotation of genes. ... "Journal of Molecular Biology. 196 (2): 261-282. doi:10.1016/0022-2836(87)90689-9. PMID 3656447.. ... length of sequence. {\displaystyle ({\text{number of }}C*{\text{number of }}G)/{\text{length of sequence}}}. [6]. or ...
Heidelberg: European Molecular Biology Organization.. *^ a b Roberts, Richard John (1969). Phytochemical studies involving ... Chow, Louise T.; Gelinas, Richard E.; Broker, Thomas R.; Roberts, Richard J. (1977). "An amazing sequence arrangement at the 5 ... "COMBREX: A project to accelerate the functional annotation of prokaryotic genomes". Nucleic Acids Research. 39 (Database issue ... Sir Richard John Roberts (born 6 September 1943) FRS[5] is an English biochemist and molecular biologist. He was awarded the ...
Functional analysis is done by comparing the recovered sequences to databases of metagenomic annotations such as KEGG. The ... After the amplicons are sequenced, molecular phylogenetic methods are used to infer the composition of the microbial community ... Targeted amplicon sequencingEdit. Targeted amplicon sequencing relies on having some expectations about the composition of the ... Recent studies use shotgun Sanger sequencing or pyrosequencing to recover the sequences of the reads.[56] The reads can then be ...
"The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. Bibcode:2006Natur.441..315G. doi ... Molecular geneticsEdit. DNA, the molecular basis for biological inheritance. Each strand of DNA is a chain of nucleotides, ... Next-generation sequencing (or high-throughput sequencing) came about due to the ever-increasing demand for low-cost sequencing ... DNA sequencing and genomicsEdit. DNA sequencing, one of the most fundamental technologies developed to study genetics, allows ...
As of 2014, the miRBase web site,[26] an archive of miRNA sequences and annotations, listed 28,645 entries in 233 biologic ... Bagasra O, Prilliman KR (August 2004). "RNA interference: the molecular immune system". Journal of Molecular Histology. 35 (6 ... transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences". Molecular ... When other dsRNA sequences were tested against DvSnf7, the other sequences were no longer effective which suggests that ...
The suffix -ome as used in molecular biology refers to a totality of some sort; it is an example of a "neo-suffix" formed by ... and sequencing methods that find chemical modification of cytosines, like bisulfite sequencing. ... Proteomics data used for gene annotations.. *Structural genomics: Study of 3-dimensional structure of every protein encoded by ... The association with chromosome in molecular biology is by false etymology. The word chromosome derives from the Greek stems ...
2006). "The DNA sequence and biological annotation of human chromosome 1.". Nature. 441 (7091): 315-21. PMID 16710414. doi: ... Gibbs S، Fijneman R، Wiegant J، van Kessel AG، van De Putte P، Backendorf C (Aug 1993). "Molecular characterization and ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.". Proc. Natl. Acad. Sci. U.S.A ...
Molecular dynamics simulations can be used to estimate a systems's statistical ensemble so that it can be analyzed with the ... function and related annotation for allosteric molecules. Currently, ASD contains allosteric proteins from more than 100 ... This is particularly useful for GPCRs where selective orthosteric therapy has been difficult because of sequence conservation ... allows for the domains to have any number of states and the contribution of a specific molecular interaction to a given ...
FAM107A: Family with sequence similarity 107 member A. *FAM19A1: Family with sequence similarity 19 member A1, C-C motif ... Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2. .. ... Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome ... varies (for technical details, see gene prediction). Among various projects, the collaborative consensus coding sequence ...
2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-321. doi:10.1038/nature04727 ... Molecular function. • GTPase activator activity. • GTPase activity. Cellular component. • cytoplasm. • cytosol. • cell nucleus ... RGS 13 is a member of R4 subfamily of RGS (Regulators of G Protein Signaling) proteins which have only short peptide sequences ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A ...
Molecular Biology Databases. *REBASE ref# 15306 - REBASE - The Restriction Enzyme Database. Research Materials. *online strain ... Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome.. Kontur WS1, Schackwitz WS, Ivanova N, Martin J, ... The DNA sequences of chromosomes I and II of Rhodobacter sphaeroides strain 2.4.1 have been revised, and the annotation of the ... Errors in the originally published sequence have been corrected, and ~11% of the coding regions in the original sequence have ...
Structure (Molecular Modeling Database). *Vector Alignment Search Tool (VAST). *All Domains & Structures Resources... ... Whole-Genome Sequencing and Annotation of Bacillus safensis RIT372 and Pseudomonas oryzihabitans RIT370 from Capsicum annuum ( ... Annotation revealed gene clusters for the synthesis of bacilysin, lichensin, and bacillibactin and sporulation killing factor ( ... Here, we report the genome sequences of Bacillus safensis RIT372 and Pseudomonas oryzihabitans RIT370 from Capsicum spp. ...
Mutation Annotation.. Several custom scripts were written to annotate candidate variants. The coordinates of protein-coding ... Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing ... Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing ... The reference genome sequence was NCBI Reference Sequence NC_000913.2. For each sample, Illumina reads were aligned to the E. ...
Gene Annotation.. The repeat-masked HSY and X sequences were blasted to the papaya EST and gene model databases, and EST ... Individual BAC clones were sequenced using Sanger sequencing method. Escherichia coli genomic sequences, vector sequences, low ... close to the sequencing error of 1 per 105 nucleotides (SI Appendix, Fig. S2B). The molecular HSY border B, where sequence ... Sequencing papaya X and Yh chromosomes reveals molecular basis of incipient sex chromosome evolution. Jianping Wang, Jong-Kuk ...
The addition of descriptive information about the function or structure of a molecular sequence to its molecular sequence data ... Protein Data- Molecular Sequence Annotation. MeSH ID: D058977 Description:. ... data_type/protein_data/molecular_sequence_annotation.txt. · Last modified: 2021/04/23 18:53 by samantha. ... Sequence annotation may be added to repositories such as DNA Databank of Japan, European Nucleotide Archive, GenBank, Gene ...
... and functions are also assigned to sequences with GO annotations as part of the annotation process. The annotations were ... Functional annotation. Functional annotation of the assembled sequences was performed using the Blast2GO program with default ... Sequencing, assembly, and functional annotation of newt expression sequence tags. As mentioned previously dedifferentiation ... The initial set of cDNA sequence reads were 10,449 (Table 1). The total length of these sequences was 9.85 Mb, which was ...
Data analysis and variant annotation. The data from a sequencing run were processed using the GS Run Processor application to ... sequencing plate (PTP). The sequencing run was prepared as described in the Sequencing Method Manual (GS Junior Titanium Series ... Molecular diagnosis for heterogeneous genetic diseases with targeted high-throughput DNA sequencing applied to retinitis ... Each adaptor included a unique sequence of ten nucleotides (called the molecular identifier, MID) to distinguish each sample ...
Sequence alignment, variant detection, and annotation. Illumina reads were aligned to the GRCh37 reference human genome ... All samples were sequenced at the Broad Institute Sequencing Platform. Genomic DNA was sheared, ligated to Illumina sequencing ... Molecular Diagnosis of Infantile Mitochondrial Disease with Targeted Next-Generation Sequencing. By Sarah E. Calvo, Alison G. ... Molecular Diagnosis of Infantile Mitochondrial Disease with Targeted Next-Generation Sequencing. By Sarah E. Calvo, Alison G. ...
Meanwhile, the molecular regulatory basis of fat accumulation by BSF is still unclear; it is necessary to identify vital genes ... By Illumina sequencing, 218,295,450,000 nt were generated. Through assembly by Trinity, 70,475 unigenes were obtained with an ... Therefore, to provide insight into this unexplained phenomenon, the molecular regulation of rapid fat accumulation by BSF ... The study provides an unprecedented level of insight from transcriptome sequencing to reveal the crude fat accumulation ...
molecular biology. *microscopy. *DNA sequencing. *genome annotation. *comparative and functional genomics. an Opportunity for ... and submit the annotated sequences to the National Center for Biotechnology Information GenBank database. As a capstone ...
Sequences are plotted by the year when they were originally deposited in the database (x-axis). The number of sequences (left y ... Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.. Schnoes AM1, Brown SD, ... The number of sequences found to be misannotated is shown in red. The bars for each year represent only the sequences deposited ... Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies ...
This webinar will discuss novel long-read transcript sequencing (LRTseq) methods for transcriptome annotation that could ... Novel Methods for Improving De Novo Transcriptome Annotation with Long-Read Transcript Sequencing. ... Sequencing workflows require library quantification and normalization to ensure data quality and reduce cost. ... Miraculins, Fox Chase to Validate Europroteomes Colorectal Biomarker Panel as Molecular Diagnostic. Jun 15, 2006 ...
This webinar will discuss novel long-read transcript sequencing (LRTseq) methods for transcriptome annotation that could ... Novel Methods for Improving De Novo Transcriptome Annotation with Long-Read Transcript Sequencing. ... Integrating Molecular Tests With EMRs Seen as Essential to Advancing Precision Diagnostics. Oct 11, 2016 ... In 2016, the Association for Molecular Pathology (AMP), in partnership with the College of American Pathologists (CAP) and ...
Molecular Sequence Annotation * Phosphorylation * Protein Array Analysis / methods* * Protein Interaction Maps * Protein-Serine ... 2017 by The American Society for Biochemistry and Molecular Biology, Inc. Publication types * Research Support, N.I.H., ... Functional annotation analysis suggested that these proteins have a variety of functions, including metabolic process, kinase ... 1 From the ‡Department of Biochemistry and Molecular Biology, Sun Yat-Sen University Zhongshan School of Medicine, Sun Yat-Sen ...
Molecular Sequence Annotation * Organ Specificity * Quantitative Trait Loci * Tissue Banks * United States ...
Cozzetto, Domenico; Jones, David T. (2017). "Computational Methods for Annotation Transfers from Sequence". In Dessimoz, C; ... molecular function, the elemental activities of a gene product at the molecular level, such as binding or catalysis; ... Annotation[edit]. Genome annotation encompasses the practice of capturing data about a gene product, and GO annotations use ... Annotations from automated processes (for example, remapping annotations created using another annotation vocabulary) are given ...
Phytopathogenic fungi ; Molecular identification ; ITS ; Taxonomy ; Annotation Ämneskategorier. Mikrobiologi, Botanik, ... Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, ... However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution ... including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis ...
Table 1 Summary of RNA sequencing, assembling, and functional annotation for D. antiqua. ... 2013 Transcriptome sequencing as a platform to elucidate molecular components of the diapause response in the Asian tiger ... The molecular regulation of the ontogenesis transition remains largely unknown. Here we used high-throughput RNA sequencing to ... Global Transcriptome Sequencing Reveals Molecular Profiles of Summer Diapause Induction Stage of Onion Maggot, Delia antiqua ( ...
... and annotation; RNA expression and secondary structure; protein structure and folding; and molecular interactions and dynamics. ... It covers subjects such as the sequence alignment algorithms: dynamic programming, hashing, suffix trees, and Gibbs sampling. ... 18.417 Introduction to Computational Molecular Biology (MIT). This course introduces the basic computational methods used to ... Furthermore, it focuses on computational approaches to: genetic and physical mapping; genome sequencing, assembly, ...
... and annotation; RNA expression and secondary structure; protein structure and folding; and molecular interactions and dynamics. ... It covers subjects such as the sequence alignment algorithms: dynamic programming, hashing, suffix trees, and Gibbs sampling. ... molecular biology, and cell biology. Biological function at the molecular level is particularly emphasized and covers the ... 18.417 Introduction to Computational Molecular Biology (MIT). This course introduces the basic computational methods used to ...
Complete DNA sequences can be used as a platform to develop rapid epidemiologic tools to identify and trace the spread of ... The sequence was a 93,629-bp plasmid encoding a single antimicrobial drug resistance gene, blaCTX-M-14. From this information, ... Whole-plasmid sequencing showed that pCT was 93,629 bp (Figure 1) with an average G+C content of 52.67%. Annotation of the ... Complete DNA sequence plasmid comparisons. Bands of color indicate homology between sequences. Red lines show sequence in... ...
Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These ... Protein structure annotation using sequence profiles * POLYVIEW-3D. Versatile annotation and high quality visualization of ... Align proteins by sequence and 3D structure. * Swiss PDB viewer A 3D graphics and molecular modeling program for the ... Zeus provides a sequence search that can highlight within the molecular structure. Ramachandran plots of internal dihedral ...
Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These ... Sequence Length. Organism. Details. Image. PROTEIN (PPAR-DELTA). A, B. 271. Homo sapiens. Mutation(s): 0 Gene Names: PPARD, ... Molecular recognition of fatty acids by peroxisome proliferator-activated receptors.. Xu, H.E., Lambert, M.H., Montana, V.G., ... These structures provide molecular insight into the propensity for PPARs to interact with a variety of synthetic and natural ...
Basic concepts of molecular biology: genomes, transcripomes, proteomes.. Sequence analysis: genome annotation, sequence ... To introduce the data that arises from studies in molecular biology. To reinforce the theory underlying the concepts and ... The module introduces basic concepts of molecule biology, sequence analysis and genomic era biology. It introduces a number of ... techniques of sequence analysis and post-genomic bioinformatics. An understanding of the distributed and available resources ...
Specifically binds to the 5-TCAT-3 DNA sequence. Has transcription repressor activity in vitro (By similarity). ... the date of the last sequence update and the date of the last annotation modification (Last modified). The version number for ... www.uniprot.org/help/sequences">molecular weight,/a>. The information is filed in different subsections. The current ... Reviewed-Annotation score: Annotation score:3 out of 5. ,p>The annotation score provides a heuristic measure of the annotation ...
... help/sequence_similarities target=_top>More...,/a>,/p>Sequence similaritiesi. Belongs to the ETS family.UniRule annotation. ... Molecular function. DNA-bindingUniRule annotation. ,p>Information which has been generated by the UniProtKB automatic ... Annotation score: Annotation score:2 out of 5. ,p>The annotation score provides a heuristic measure of the annotation content ... Annotation score: Annotation score:1 out of 5. ,p>The annotation score provides a heuristic measure of the annotation content ...
Molecular Sequence Annotation. Multigene Family / genetics. Onygenales / genetics*, pathogenicity. Phylogeny. Protein Structure ... The Maker annotation pipeline [9] was used to annotate the A. apis genome [7]. Maker masked repetitive sequences with ... Following the sequencing of the A. apis genome in 2006 [7], our comprehensive, transcriptome-informed gene annotations ... Manual annotation methods Transcripts were compared to sequences in GenBank. TBLASTX and BLASTX searches were done against ...
Sequence alignment, multiple alignment. *Genome annotation, metagenomics. *Gene expression analysis. *Qualitative and ... Course "Bioinformatics: computer methods in molecular and systems biology". Trieste, Italy25 -29 June 2018 ... Based on a structured overview of bioinformatics methods this course gives an introduction to the main concepts of sequence ... bioinformatics applied to next generation sequencing and proteomics data. The course contains theoretical and practical ...
Strozzi F, Mazza R, Malinverni R, Williams JL (February 2009). "Annotation of 390 bovine miRNA genes by sequence similarity ... In molecular biology miR-181 microRNA precursor is a small non-coding RNA molecule. MicroRNAs (miRNAs) are transcribed as ~70 ... International Chicken Genome Sequencing Consortium (December 2004). "Sequence and comparative analysis of the chicken genome ... "Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of ...
  • 1 From the ‡Department of Biochemistry and Molecular Biology, Sun Yat-Sen University Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China. (nih.gov)
  • To introduce the data that arises from studies in molecular biology. (ncl.ac.uk)
  • The module introduces basic concepts of molecule biology, sequence analysis and genomic era biology. (ncl.ac.uk)
  • Basic concepts of molecular biology: genomes, transcripomes, proteomes. (ncl.ac.uk)
  • In molecular biology miR-181 microRNA precursor is a small non-coding RNA molecule. (wikipedia.org)
  • Computational biology is a rapidly expanding field, and the number and variety of computational methods used for DNA and protein sequence analysis is growing every day. (elsevier.com)
  • We do research in bioinformatics, applying computational approaches to problems in molecular biology. (yale.edu)
  • Resolving the programs controlling these changes at the molecular level can provide important insights into the principles of human biology and disease. (mcponline.org)
  • Molecular Biology and Evolution 7:607-633. (grisda.org)
  • Sequence editing is such a primary part of molecular biology research that it may seem like any sequence editing software will do. (dnastar.com)
  • Our broad English-language curriculum includes lectures and seminars in the life sciences and extensive hands-on training in brand new molecular biology and bioinformatics teaching laboratories. (molbiol.ru)
  • ACGT, Inc., a DNA sequencing and molecular biology service provider located in the north Chicago suburbs, has a position available for a Bioinformatics Analyst. (bioinformatics.org)
  • Knowledge, background, or experience in molecular biology and microbiology. (bioinformatics.org)
  • General molecular biology techniques (western blotting, qPCR, in situ hybridisation etc. (niab.com)
  • It is also key to event identification and correlation in domains as diverse as high-energy physics and molecular biology. (acm.org)
  • Comparative Biochemistry and Physiology B-Biochemistry & Molecular Biology 169, 38-50. (auburn.edu)
  • If your first degree included the study of genetics and molecular biology, and a research module, you're well-placed to join us. (northumbria.ac.uk)
  • With the increasing amount of DNA sequence information deposited in public databases, searching for similarity to a query sequence has become a basic operation in molecular biology. (psu.edu)
  • The Molecular Biology Database Collection: 2005 update. (vldb.org)
  • Students from participating colleges and universities isolate and characterize bacteriophages from local environments, annotate the phage genomes, and submit the annotated sequences to the National Center for Biotechnology Information GenBank database. (hhmi.org)
  • Direct detection of translated peptides by tandem mass spectrometry methods has proved valuable in the annotation of genomes as they allow prediction or refinement of gene structures and can resolve difficulties in annotating from cDNA alternative splice forms and overlapping gene sequences ( 14 - 18 ). (mcponline.org)
  • The group has multiple missions: formatting of the data generated by the sequencers, data quality control, assembly of genomes and transcriptomes, annotation of eukaryote genomes. (cea.fr)
  • THE sequencing of whole genomes of species from all kingdoms of life progresses at an ever increasing pace. (genetics.org)
  • To determine the genetic basis for chemotype-specific differences in toxin production, the genomes of four Stachybotrys strains were sequenced and assembled de novo. (nih.gov)
  • 15]). The genomes of these four strains were obtained by massive parallel sequencing on an Illumina Hiseq 2000. (nih.gov)
  • We report complete genome sequencing and analysis, and genetic tool development suitable for expression of transgenes inserted into the nuclear or chloroplast genomes. (nature.com)
  • We have recently released annotations for more than 50 animal genomes for an update of our database of selenoproteins. (mpg.de)
  • The i5k, an initiative to sequence the genomes of 5,000 insect and related arthropod species, is a broad and inclusive effort that seeks to involve scientists from around the world in their genome curation process, and Apollo is serving as the platform to empower this community. (slideshare.net)
  • However, existing analytical approaches focus on attributing sequencing reads to known genes/genomes, often failing to make maximal use of available data. (uni-kiel.de)
  • To account for the great diversity of domain contexts and an unexpected paucity of ortholog conservation, we must categorize the coding regions of completely sequenced genomes into domain families, as well as protein families. (biomedcentral.com)
  • Software for the automatic annotation of eukaryotic genomes. (biomedcentral.com)
  • Over the last two decades, candidate genes associated with adRP in individual patients have been screened for mutations in different populations, using a variety of methods, including single-strand conformational polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), and denaturing high-performance liquid chromatography (DHPLC) followed by direct genomic sequencing. (molvis.org)
  • We performed "MitoExome" sequencing of the mitochondrial DNA (mtDNA) and exons of ~1000 nuclear genes encoding mitochondrial proteins and prioritized rare mutations predicted to disrupt function. (sciencemag.org)
  • Advances in next-generation sequencing (NGS) technology are facilitating the discovery of new disease genes and promise to transform the routine clinical diagnosis of inherited disease. (sciencemag.org)
  • Although sequence-based clinical diagnosis has long been available for individual genes, NGS could be particularly useful for conditions characterized by genetic heterogeneity, where individual genes cannot be readily prioritized for traditional sequencing. (sciencemag.org)
  • Here we used high-throughput RNA sequencing to identify candidate genes and processes linked to summer diapause (SD) induction by comparing the transcriptome differences between the most sensitive larval developmental stage of SD and nondiapause (ND). (g3journal.org)
  • The utility of the genome sequence increases with the quality of annotation of protein-encoding genes. (mcponline.org)
  • Once a full genome has been assembled, the main challenge lies in its annotation, i.e. , in identifying the protein-coding genes and other functional units that are encoded in the genome. (genetics.org)
  • How to design and analyze oligonucleotide primers for discovering genes in organisms where they have not been identified when the gene's encoded protein sequence is known in other organisms. (fsu.edu)
  • Molecular characterization, phylogenetic analysis and expression profiling of myoglobin and cytoglobin genes in response to heat stress in channel catfish Ictalurus punctatus. (auburn.edu)
  • Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. (springer.com)
  • Frédéric Romagné is working on the identification and correct annotation of selenoprotein genes. (mpg.de)
  • Learn to identify homologs of known genes of interest in your newly sequenced genome. (slideshare.net)
  • We created faser (functional annotation of sequencing reads), an algorithm that is optimized to map reads to molecular functions encoded by the read-correspondent genes. (uni-kiel.de)
  • A search of the M1genome sequence, which includes 97% of the Myxococcus xanthus genes, identified 53 sequence homologs of σ 54 -dependent enhancer binding proteins (EBPs). (asm.org)
  • The evolutionary history of eukaryotic proteins involves rapid sequence divergence, addition and deletion of domains, and fusion and fission of genes. (biomedcentral.com)
  • This allows for the identification of core biosynthetic enzymes using genome mining strategies that are based on the sequence similarity of the involved enzymes/genes. (dtu.dk)
  • Compilation of tRNA sequences and sequences of tRNA genes. (vldb.org)
  • Our goal was to perform whole-exome sequencing (WES) to examine variants in known IRD genes in underrepresented African cohorts. (arvojournals.org)
  • Variants in reported IRD genes were identified using WES and validated by Sanger sequencing. (arvojournals.org)
  • The system was developed with two goals: (i) to acquire the mixed plasmid-enriched genomic sequence of B. thuringiensis using next-generation sequencing biotechnology, and (ii) to identify cry genes with a computational pipeline (using BtToxin_scanner). (asm.org)
  • The pipeline proved to be fast (average speed, 1.02 Mb/min for proteins and open reading frames [ORFs] and 1.80 Mb/min for nucleotide sequences), sensitive (it detected 40% more protein toxin genes than a keyword extraction method using genomic sequences downloaded from GenBank), and highly specific. (asm.org)
  • Twenty-seven candidate sequences were selected on the basis of their low level of sequence identity to known cry genes, and eight full-length genes were obtained with PCR. (asm.org)
  • Functional annotation analysis suggested that these proteins have a variety of functions, including metabolic process, kinase activity and phosphorylation, cell growth, apoptosis and cell death, and immunity, indicating a pleiotropic role of ROP18 kinase. (nih.gov)
  • Structures can be downloaded and displayed from the PubChem, PDB, and NCBI structure databases together with the sequences for proteins and nucleic acids. (rcsb.org)
  • We detected 1384 proteins from 327,906 peptide sequence identifications at 72 and 120 hpf with false identification rates of less than 1% using 2D LC-ESI-MS/MS. These included only ∼30% of proteins that were identified by 2D PAGE-MALDI-TOF/TOF. (mcponline.org)
  • Bioinformatics annotation methods combined with GCxGC/MS-based metabolomics and LC/MS-based shotgun proteomics profiling technologies have been applied to characterize abundant proteins and metabolites, resulting in the detection of 1069 proteins and 159 metabolites. (genetics.org)
  • By integrating genomic annotation information with experimentally identified metabolites and proteins, we constructed a draft metabolic network for Chlamydomonas. (genetics.org)
  • Despite its many limitations and problems, whole-genome annotation has become a standardized data flow and initial sets of all encoded proteins can be generated in a computer-assisted and automated way. (genetics.org)
  • Although accurate measurement of molecular mass values assures protein identification in many cases, it only allows for reliable identification of isolated proteins of relatively simple mixtures. (mcponline.org)
  • Our targets are mainly selected from the complete set of soluble Mycoplasma proteins and their prokaryotic homologs that have no significant sequence similarity to proteins of known structure. (strgen.org)
  • On the other, we use population genetics and molecular evolution approaches to study the evolution of the use of selenocysteine, the selenium-containing amino acid, compared to cysteine in proteins. (mpg.de)
  • Based on a structured overview of bioinformatics methods this course gives an introduction to the main concepts of sequence bioinformatics applied to next generation sequencing and proteomics data. (icgeb.org)
  • The integration of metabolomic and proteomics technologies into the annotation process may lead to further experimental validation of in silico gene models as well as to improved accuracy of existing gene models. (genetics.org)
  • Like EST sequencing, proteomics methods provide actual evidence for the presence of gene products and thus can serve as validation of gene models. (genetics.org)
  • I employ functional genomics tools such as proteomics and RNA-sequencing to study genome responses in a spontaneous and severe asthma-like disease affecting horses in the southern US- Equine Pasture Asthma (previously Summer Pasture Associated Recurrent Airway Obstruction). (msstate.edu)
  • Pathogen Surveillance and Characterization using Whole Genome Sequencing: The Colorado Cystic Fibrosis Research and Development Program - Molecular and Genomics Core. (nationaljewish.org)
  • Morphological and molecular characterization of Brazilian populations of Diatraea saccharalis (Lepidoptera: Crambidae) and the evolutionary relationship among Diatraea spp. (usda.gov)
  • Established models will then be sequenced by NCI-funded Genome Characterization Centers (GCCs) and molecular and clinical data will be made available through the NCI Genomic Data Commons (GDC). (nih.gov)
  • The study provides an unprecedented level of insight from transcriptome sequencing to reveal the crude fat accumulation mechanism in developing BSF. (springer.com)
  • Our transcriptome analysis provides insight into the fundamental role of the circadian clock in SD induction in this important model insect species, and contributes to the in-depth elucidation of the molecular regulation mechanism of insect diapause induction. (g3journal.org)
  • This webinar will discuss novel long-read transcript sequencing (LRTseq) methods for transcriptome annotation that could increase the efficiency and accuracy of future sequencing projects. (genomeweb.com)
  • RESULTS: We compared A. apis transcriptome sequence from mycelia grown on liquid or solid media with that dissected from host-infected tissue. (biomedsearch.com)
  • An adequate quantity of originating tumor (=50 mg) is required so that its genome and transcriptome can be sequenced with standard protocols and a model can be developed. (nih.gov)
  • We have used transcriptome sequencing to systematically elucidate the contents the C. geographus venom duct, dividing it into four segments in order to investigate each segment's mRNA contents. (biomedcentral.com)
  • Thus, our transcriptome analysis provides a new physiological framework for understanding the molecular envenomation strategy of this deadly snail. (biomedcentral.com)
  • Experience in de novo sequence analysis, re-sequencing, RNA-Seq. (bioinformatics.org)
  • This talk will highlight how De novo transcreiptome sequencing enables to explore rare and non-genetically characterized plants obtained in situ and identify its genetic coding complement. (selectbiosciences.com)
  • The sequencing data were de novo assembled, and a total of 113 candidate cry sequences were identified using the computational pipeline. (asm.org)
  • Broadly, we are interested in large-scale analyses of genome sequences, macromolecular structures, and functional-genomics datasets. (yale.edu)
  • Pseudogenes provide a contrasting annotation to binding sites and ncRNAs in being derived from comparative rather than functional genomics data. (yale.edu)
  • However, the use of these sequenced varieties for functional genomics analyses is limited by their long life cycles or low transformation efficiencies. (springer.com)
  • In 2016, the Association for Molecular Pathology (AMP), in partnership with the College of American Pathologists (CAP) and American College of Molecular Genetics (ACMG), launched a set of guidelines meant to set industry standards for reporting of molecular diagnostic test results in oncology, using a tier-based system and defined levels of evidence. (genomeweb.com)
  • The zebrafish ( Danio rerio ) is an attractive vertebrate model organism for studies into the molecular mechanisms of development ( 2 ), pathology ( 3 ), and pharmacology ( 4 , 5 ). (mcponline.org)
  • The job will involve a diverse skill set which will set up an early career researcher interested in pursuing a career in molecular genetics and pathology. (niab.com)
  • rather, sequences are annotated using computational analysis. (nih.gov)
  • This course introduces the basic computational methods used to understand the cell on a molecular level. (nottingham.ac.uk)
  • Computational and manual annotations have been made publicly available on the Bee Pests and Pathogens website. (biomedsearch.com)
  • Genome annotations are supported by alignments of experimentally documented transcript or protein sequences specific for the zebrafish genome, by alignments of homologous transcript or protein sequences, and ab initio by computational gene prediction ( 10 ). (mcponline.org)
  • 4) visualization and annotation techniques for multiple sequence alignments. (fsu.edu)
  • S4: structure-based sequence alignments of SCOP superfamilies. (vldb.org)
  • Molecule World for iPhone can be used on the iPhone or iPod touch to display and manipulate 3D chemical and molecular structures from the PubChem, PDB, or NCBI structure databases. (rcsb.org)
  • Our sequence editing software is also integrated with NCBI databases, making it easy to access and search online databases. (dnastar.com)
  • Sequence analysis: genome annotation, sequence alignment, multiple sequence alignment. (ncl.ac.uk)
  • Techniques used include basic multiple sequence alignment, consensus creation, back translation, and primer discovery and evaluation. (fsu.edu)
  • Multiple sequence alignment, expectation maximization, profiles, and Markov models ( pdf ) ( supplemental lecture pdf ) ( Lab Report #7 ). (fsu.edu)
  • How to use PAUP* (Phylogenetic Analysis Using Parsimony [and Other Methods], PHYLIP (PHYLogeny Inference Package), and other tools to ascertain and draw phylogenetic trees from multiple sequence alignment datasets. (fsu.edu)
  • Molecular Evolution, Multiple Sequence Alignment & Phylogenetics. (slideserve.com)
  • Molecular Evolution, Multiple Sequence Alignment & Phylogenetics.Canadian Bioinformatics Workshop Thursday June 21st David Lynn M.Sc. (slideserve.com)
  • p>Manual validated information which has been generated by the UniProtKB automatic annotation system. (uniprot.org)
  • The results - a total of 31,954 changes - are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. (gu.se)
  • In this study, we report the full sequence and analysis of pCT and demonstrate the spread of pCT-like plasmids in animal and human E. coli isolates from the United Kingdom, Europe, Australia, and Asia. (cdc.gov)
  • To reinforce the theory underlying the concepts and techniques of sequence analysis and post-genomic bioinformatics. (ncl.ac.uk)
  • Alkahest is an initiative to produce free open source software systems for high-throughput DNA sequence data management and analysis. (bioinformatics.org)
  • 3. An introduction to biological sequence analysis (K.H. Fasman, S.L. Salzberg). (elsevier.com)
  • 6. Classification-based molecular sequence analysis (D.J. States, W.C. Reisdorf, Jr.) 7. (elsevier.com)
  • 12. Analysis and algorithms for protein sequence-structure alignment (R.H. Lathrop et al. (elsevier.com)
  • Thus, genomic sequencing and phylogenomic analysis of isolates is essential to identify outbreaks and limit their occurrence and spread. (nationaljewish.org)
  • geWorkbench is an open-source bioinformatics platform that offers a comprehensive and extensible collection of tools for the management, analysis, visualization and annotation of biomedical data. (columbia.edu)
  • For sequence data there are routines such as BLAST, pattern detection, transcription factor mapping, and syntenic region analysis. (columbia.edu)
  • Furthermore, genomic sequences around markers of interest found in microarray experiments can be easily retrieved and, for example, used for promoter/transcription factor analysis. (columbia.edu)
  • Analysis of DNA sequences from more than 30 gene portions were used to determine similarities among five orders of mammals. (grisda.org)
  • Many groups have developed pathway analysis tools relative to annotation and identification. (psu.edu)
  • The group interacts with the Genoscope laboratories: sequencing, technological development team (development of new protocols and set up of new sequencers) and research team (analysis). (cea.fr)
  • We present an integrated analysis of the molecular repertoire of Chlamydomonas reinhardtii under reference conditions. (genetics.org)
  • Perform basic and advanced analysis on data produced from next generation sequencing systems (DNA-seq, RNA-seq, metagenomics, ChIP-seq, etc.) as well as genotyping and gene expression microarrays. (bioinformatics.org)
  • Experience with the relevant sequence analysis tools/best practices. (bioinformatics.org)
  • large scale data analysis and sequence assembly and annotation experience is a plus. (bioinformatics.org)
  • How to get sequencing fragment data from an automated sequencer into the computer and assembled into a contiguous sequence (contig) using GCG's SeqMerge, and then how to perform restriction enzyme mapping and compositional analysis on that contig for subcloning and other purposes. (fsu.edu)
  • Gene identification and analysis of transcripts differentially regulated in fracture healing by EST sequencing in the domestic sheep. (mpg.de)
  • Application of sequence based and structure-based approaches to assignment of gene functions - e.g. sequence comparison, structure analysis (especially active sites, binding sites) and comparison, pattern identification, etc. (successcds.net)
  • Functional sequencing read annotation for high precision microbiome analysis. (uni-kiel.de)
  • The mi-faser microbiome analysis pipeline, combining faser with our manually curated reference database of protein functions, accurately annotates microbiome molecular functionality. (uni-kiel.de)
  • The advent of molecular techniques for phylogenetic analysis transformed understanding of oak relationships, initially by uncovering molecular support for the diphyletic division of Quercus into Old World and New World clades. (wikipedia.org)
  • the two other protein sequence databases (GenBank NR and TrEMBL) and the protein sequences in the KEGG pathways database exhibit similar and surprisingly high levels of misannotation that average 5%-63% across the six superfamilies studied. (nih.gov)
  • Recent application of molecular genetic tools for the exploration of the metabolism of Desulfovibrio vulgaris Hildenborough has provided several new datasets that might provide insights and constraints to the electron flow pathways. (frontiersin.org)
  • The annotation of biochemical pathways resulted in a total of 11,971 unigenes assigned with 145 KEGG maps and 1759 enzyme codes. (frontiersin.org)
  • 8. The gene: a "moving target" "The gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products. (slideshare.net)
  • It covers subjects such as the sequence alignment algorithms: dynamic programming, hashing, suffix trees, and Gibbs sampling. (nottingham.ac.uk)
  • Learn to use the GLAM2 algorithm (Gapped Local Alignment of Motifs), which is part of a motif discovery tool that can detect conserved motifs in a set of DNA or protein sequences that you provide. (openhelix.com)
  • This may include sequence alignment, large-scale or complex queries, motif finding, or comparative assessments. (openhelix.com)
  • Sequence annotation may be added to repositories such as DNA Databank of Japan , European Nucleotide Archive , GenBank , Gene Ontology Annotation Database , PeptideAtlas , The Protein Database , UniProt , and VectorBase . (dataseer.ai)
  • We have investigated the misannotation levels for molecular function in four public protein sequence databases (UniProtKB/Swiss-Prot, GenBank NR, UniProtKB/TrEMBL, and KEGG) for a model set of 37 enzyme families for which extensive experimental information is available. (nih.gov)
  • SeqBuilder Pro supports virtually any type of sequence file, including FASTA, ABI, and GenBank formats, and easily imports files from Vector NTI , SnapGene, and Geneious. (dnastar.com)
  • 2015. Evolutionary Molecular Genetic Clocks: A Perpetual Exercise in Futility and Failure . (icr.org)
  • Genome sequence and genetic diversity of the common carp, Cyprinus carpio. (auburn.edu)
  • information, including chromosome, genetic and molecular maps. (biomedcentral.com)
  • Our study identified genetic defects in almost 40% of the families analyzed, significantly enhancing the molecular diagnosis of IRD in South Africa. (arvojournals.org)
  • Uniquely positioned within this shifting healthcare paradigm are molecular and clinical laboratories that can provide healthcare teams with access to a rich repository of actionable genetic data. (darkdaily.com)
  • For SNP annotation, many kinds of genetic and genomic information are used. (wikipedia.org)
  • In this type of annotation more emphasis is given to genetic variation that disrupts the protein function domain, protein-protein interaction and biological pathway. (wikipedia.org)
  • The addition of descriptive information about the function or structure of a molecular sequence to its molecular sequence data record. (dataseer.ai)
  • Genome annotation encompasses the practice of capturing data about a gene product, and GO annotations use terms from the GO ontology to do so. (wikipedia.org)
  • Sequencing workflows require library quantification and normalization to ensure data quality and reduce cost. (genomeweb.com)
  • Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. (gu.se)
  • ANTHEDNA is a package of integrated UNIX freeware tools for retrieving and analyzing sequence data. (bioinformatics.org)
  • It is called ANTHEDNA because it was developed for analyzing the DNA sequence data obtained from the ribosomal database project. (bioinformatics.org)
  • With the advent of next-generation sequencing technologies and their application in understanding MDR pathogen dynamics, it has become imperative to unify AR gene data resources for easy accessibility for researchers. (asm.org)
  • Our research involves a number of quantitative techniques, including database design, systematic datamining and machine learning, visualization of high-dimensional data, and molecular simulation. (yale.edu)
  • We have carried out this effort by processing next-generation sequencing data (i.e. (yale.edu)
  • Most importantly, geWorkbench provides an environment which supports moving from one data type to another in a seamless fashion, e.g. from gene expression to sequences to patterns. (columbia.edu)
  • The bio-informatics R&D and sequencing team is responsible for the data, mainly sequence data, generated by the instruments. (cea.fr)
  • The principal theme of the Bioinformatics R&D and sequencing team is the processing of data generated by the new-generation sequencers. (cea.fr)
  • All data sets are made available as supplementary material as well as web-accessible databases and within the functional context via the Chlamydomonas-adapted MapMan annotation platform. (genetics.org)
  • Extraction of complementary sequence information was performed prior to data base search using in-house written software. (mcponline.org)
  • Acquired tandem mass spectra are matched against predicted fragments of all peptides that are present in a sequence data base and match the measured molecular masses ( 13 ). (mcponline.org)
  • With the Mascot program ( 14 ) or equivalent search engine, every tandem mass spectrum is assigned a list of matching data base peptide sequences accompanied by a score representing the quality of each of these sequence identifications. (mcponline.org)
  • GOblet: annotation of anonymous sequence data with Gene Ontology and pathway terms. (mpg.de)
  • This talk will illustrate few Hybrid Approaches used for assembling data from multiple sequencing platforms to form Hybrid Genome which allows one to correct for the biases and errors of one platform with information from a complementary platform. (selectbiosciences.com)
  • Molecular data and clinical data will be made available to researchers as a community resource. (nih.gov)
  • Understanding that NGS services represent a major financial commitment by laboratories, the advantages of using NGS testing as a tool to retain and grow a lab's customer base is also examined, as is the importance of purchasing a best-of-breed molecular LIS created with big data, genome annotation and interpretation, and informed decision-making in mind. (darkdaily.com)
  • Many tools available have been developed for SNP annotation in different organisms: some of them are optimized for use with organisms densely sampled for SNPs (such as humans), but there are currently few tools available that are species non-specific or support non-model organism data. (wikipedia.org)
  • 1990. Tetrapod phylogeny inferred from 18S and 28S ribosomal RNA sequences and a review of the evidence for amniote relationships. (grisda.org)
  • A. The conceptual phylogeny shows the toxin chemotypes of the four sequenced Stachybotrys strains in relation to other trichothecene-producing fungi of order Hypocreales. (nih.gov)
  • The phylogeny of the four Stachybotrys strains that were sequenced is shown in Figure 2A. (nih.gov)
  • However, little work has been performed to elucidate the molecular basis of diapause induction in this species. (g3journal.org)
  • Transcript contigs, protein sequences from multiple fungal species, and ab initio gene predictions were included as evidence sources in the Maker gene prediction pipeline, resulting in 6,992 consensus gene models. (biomedsearch.com)
  • The primary goal of the Molecular Core is to characterize the diversity and prevalence of NTM species affecting the CF community, and to accurately identify and limit potential instances of patient-to-patient transmission or nosocomial acquisition events in CF Centers. (nationaljewish.org)
  • 1990. Chloroplast DNA sequence from a Miocene Magnolia species. (grisda.org)
  • This DNA was sequenced and compared with an extant species of Magnolia , and some other close relatives. (grisda.org)
  • This paper reports ribosomal RNA (5S rRNA) sequences from three species of green algae. (grisda.org)
  • Similarities in ribosomal RNA sequence were investigated for 15 species of amphibians, 4 species of reptiles, and 2 species of birds. (grisda.org)
  • These were compared with published sequences for one species of amphibian and four species of mammals. (grisda.org)
  • The strains include two species, S. chlorohalonata (IBT strain 40285) and S. chartarum (IBT strains 40288, 40293, and 7711), which are distinguishable both by morphology and molecular markers. (nih.gov)
  • Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene. (ucsc.edu)
  • Sequence similarity analyses and annotation of the unigenes against non-redundant protein (Nr) and Gene Ontology (GO) databases identified 175,882 GO annotations. (frontiersin.org)
  • Furthermore, we discuss important caveats such as rule-based BGC detection, sequence and annotation quality and cluster boundary prediction, which all have to be considered while planning for, performing and analyzing the results of genome mining studies. (dtu.dk)
  • The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines. (vldb.org)
  • Our group previously employed these methods to achieve molecular diagnosis of 23.5% (52 of 221) of families with adRP in a Spanish population. (molvis.org)
  • Samples are analyzed using whole genome sequencing (WGS) and comparative phylogenomic methods. (nationaljewish.org)
  • Through genome sequencing of up to 1000 strains you will explore the genomic features within these populations and apply methods to understand gene flow and environmental reservoirs of plant pathogenic and epiphytic bacteria. (niab.com)
  • Based on the different features used by each annotation tool, SNP annotation methods may be split roughly into the following categories: Genomic information from surrounding genomic elements is among the most useful information for interpreting the biological function of an observed variant. (wikipedia.org)
  • This study aimed to test a newly devised cost-effective multiplex PCR assay for the molecular diagnosis of autosomal dominant retinitis pigmentosa (adRP), as well as the use of whole-exome sequencing (WES) to detect disease-causing mutations in adRP. (molvis.org)
  • Whole-exome sequencing was performed on 56 samples from 16 families with diverse IRD phenotypes that had remained undiagnosed after screening for known mutations using genotyping-based microarrays (Asper Ophthalmics). (arvojournals.org)
  • This work, emphasizing a mechanistic understanding of the effects of therapies on tumor evolution, provides a framework for future clinical trials testing different treatment sequences. (aacrjournals.org)
  • New CDH3 mutation in the first Spanish case of hypotrichosis with juvenile macular dystrophy, a case report Clinical-Molecular Genetics and Cytogenetics. (openhelix.com)
  • Chapter 4: What Information Technology and Informatics Capabilities Do Clinical and Molecular Laboratories Need to Succeed with NGS-based Services? (darkdaily.com)
  • For datasets still having more than one KOI, EXProt sequences whose KOIs were not identical to those of reference Escherichia coli EXProt sequences were regarded as False sequences. (psu.edu)
  • Furthermore, we generated nuclear, chloroplast, and mitochondrial genome sequences and report comparative transcriptomic analyses under low- and high-salt conditions, enabling high-resolution genome annotation and providing novel insight into the mechanisms of halotolerance. (nature.com)
  • Comparative analyses Official / Merged Gene Set Manual Annotation Automated Annotation Sequencing Assembly Synthesis & dissemination. (slideshare.net)
  • p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. (uniprot.org)
  • A total of 5773 potential simple sequence repeats (SSRs) and 3594 high-quality single nucleotide polymorphisms (SNPs) were identified. (frontiersin.org)
  • Thus one may browse sequence information, for example concerning single-nucleotide polymorphisms (SNPs), alongside both descriptions of molecular and cellular function and information relevant to human disease. (biomedcentral.com)
  • Single nucleotide polymorphism annotation (SNP annotation) is the process of predicting the effect or function of an individual SNP using SNP annotation tools. (wikipedia.org)
  • Many annotation algorithms focus on single nucleotide variants (SNVs), considered more rare than SNPs as defined by their minor allele frequency (MAF). (wikipedia.org)
  • be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein. (uniprot.org)
  • The novel multiplex PCR assay with next-generation sequencing (NGS) proved effective for detecting most of the adRP-causing mutations. (molvis.org)
  • Advances in next-generation sequencing (NGS) promise to facilitate diagnosis of inherited disorders. (sciencemag.org)
  • With the emergence of next-generation sequencing (NGS), comprehensive molecular diagnosis of RP is now within reach. (arvojournals.org)
  • This talk will highlight the Opportunities and Challenges faced in Next Generation Sequencing from Indian Perspective. (selectbiosciences.com)
  • This report reviews the main sequencing technologies and provides detailed discussion on next generation sequencing and its applications in different fields. (researchandmarkets.com)
  • With next generation sequencing (NGS) accelerating the pace of discoveries, prevention and treatment will no longer be centered around "standards of care" that often result in a predetermined sequence of therapies. (darkdaily.com)
  • The plasmid-enriched genomic DNA was extracted from these strains and mixed for Illumina sequencing. (asm.org)
  • p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence. (uniprot.org)
  • 13. THREADER: protein sequence threading by double dynamic programming (D. Jones). (elsevier.com)
  • It also lets you make a new protein sequence by translating one nucleotide sequence or thousands of them simultaneously. (dnastar.com)
  • STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database. (vldb.org)
  • Information from a known gene is used as a reference to indicate whether the observed variant resides in or near a gene and if it has the potential to disrupt the protein sequence and its function. (wikipedia.org)
  • Gene based annotation is based on the fact that non-synonymous mutations can alter the protein sequence and that splice site mutation may disrupt the transcript splicing pattern. (wikipedia.org)
  • Zebrafish genetics has been facilitated substantially by the increasing availability of genome sequence information (Sanger Institute's D. rerio sequencing project) as assembly of the 1.7-Gb genome sequence nears completion. (mcponline.org)
  • Each genome was then independently assembled with SOAPdenovo [16], followed by protein annotation of each assembly with MAKER [17] using a cross-strain iterative strategy. (nih.gov)
  • This talk will highlight the role of NGS Technologies in generating High Quality rice genome assembly and annotation. (selectbiosciences.com)
  • Initially, it will present the deep sequence of first indica cultivar, HR12 and assembly of HR12 genome using combination of Illumina's short reads and PacBio long reads which improves the quality of HR12 assembly and annotation. (selectbiosciences.com)
  • Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds (476 contigs) with a contig N50 of 1.4 Mb. (springer.com)
  • The power of whole-genome annotation approaches lies in their inherent goal of completeness. (genetics.org)
  • However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. (gu.se)
  • Some tools may also involve nucleotide sequence information. (openhelix.com)
  • The EMBL Nucleotide Sequence Database. (vldb.org)
  • This video demonstrates the plasmid auto-annotation functionality in SeqBuilder Pro which allows you to accurately and automatically annotate your sequences using a carefully curated database of features. (dnastar.com)
  • biological process , operations or sets of molecular events with a defined beginning and end, pertinent to the functioning of integrated living units: cells, tissues , organs , and organisms . (wikipedia.org)
  • 4. An introduction to hidden Markov models for biological sequences (A. Krogh). (elsevier.com)
  • Molecular Life Sciences: An Encyclopedic Reference will focus on understanding biological phenomena at the level of molecules and their interactions that govern life processes. (credoreference.com)
  • In SNP annotation the biological information is extracted, collected and displayed in a clear form amenable to query. (wikipedia.org)
  • This involves genome annotation, where one places each base within a biochemical context. (yale.edu)
  • If metabolites are being detected that, given a metabolic network derived from whole-genome annotation, actually are not reachable via the predicted network of biochemical reactions, either the enzyme annotation may be incomplete or the metabolite is synthesized by an as-of-yet-unidentified biochemical pathway. (genetics.org)
  • Complete DNA sequences can be used as a platform to develop rapid epidemiologic tools to identify and trace the spread of plasmids in clinically relevant pathogens, thus facilitating a better understanding of their distribution and ability to transfer between bacteria of humans and animals. (cdc.gov)
  • Annotation revealed gene clusters for the synthesis of bacilysin, lichensin, and bacillibactin and sporulation killing factor (skfA) in Bacillus safensis RIT372 and turnerbactin and carotenoid in Pseudomonas oryzihabitans RIT370. (nih.gov)
  • Comparative genome sequencing reveals chemotype-specific gene clusters in the toxigenic black mold Stachybotrys. (nih.gov)
  • DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants. (vldb.org)
  • The availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. (springer.com)
  • Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. (gu.se)
  • The live, interactive views in SeqBuilder Pro make it effortless to edit and annotate your sequences, customize your features and create plasmid maps . (dnastar.com)
  • The sequence annotation tools in SeqBuilder Pro make it easy annotate your sequence. (dnastar.com)