Molecular sequence annotation. Medical search

The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.

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.

The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.

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.

A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.

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.

Methods for determining interaction between PROTEINS.

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.

Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.

The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.

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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Gene based annotation is based on the fact that non-synonymous mutations can alter the protein sequence and that splice site ... Functional prediction of variants' effect in different biological processes is pivotal to pinpoint the molecular mechanism of ... Variant annotation tools use machine learning algorithms to predict variant annotations. Different annotation tools use ... SNP functional annotation is typically performed based on the available information on nucleic acid and protein sequences. ...

https://en.wikipedia.org/wiki/SNP_annotation

Cozzetto, Domenico; Jones, David T. (2017). "Computational Methods for Annotation Transfers from Sequence". In Dessimoz, C; ... Methods in Molecular Biology. Vol. 1446. Springer (New York). pp. 85-93. doi:10.1007/978-1-4939-3743-1_7. ISBN 978-1-4939-3741- ... Annotations from automated processes (for example, remapping annotations created using another annotation vocabulary) are given ... Full annotation data sets can be downloaded from the GO website. To support the development of annotation, the GO Consortium ...

https://en.wikipedia.org/wiki/Gene_Ontology

... molecular biology and bioinformatics have created the need for DNA annotation. DNA annotation or genome annotation is the ... An annotation (irrespective of the context) is a note added by way of explanation or commentary. Once a genome is sequenced, it ... PDF annotation Subject indexing Semantics Tag (metadata) Text annotation Web annotation XPS annotation "Definition of ... Annotations are sometimes presented in the margin of book pages. For annotations of different digital media, see web annotation ...

https://en.wikipedia.org/wiki/Annotation

... 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 ...

https://en.wikipedia.org/wiki/Genome_project

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 ...

https://en.wikipedia.org/wiki/GeneCards

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 ...

https://en.wikipedia.org/wiki/DNA

"A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research". Molecular Plant-Microbe ... March 2014). "Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation". Genetics ... List of sequenced eukaryotic genomes List of sequenced animal genomes List of sequenced archaeal genomes List of sequenced ... May 2017). "Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol ...

https://en.wikipedia.org/wiki/List_of_sequenced_plant_genomes

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 ...

https://en.wikipedia.org/wiki/SUHW4

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 ...

https://en.wikipedia.org/wiki/Geworkbench

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 ...

https://en.wikipedia.org/wiki/Mir-181_microRNA_precursor

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 ...

https://en.wikipedia.org/wiki/Synchytrium_endobioticum

... 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 May ...

https://en.wikipedia.org/wiki/BacMet

... 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 ...

https://en.wikipedia.org/wiki/Wojciech_Karlowski

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 ... Hedin, Marshal C.; Maddison, Wayne P. (March 2001). "A Combined Molecular Approach to Phylogeny of the Jumping Spider Subfamily ... Eperon, I. C.; Anderson, S.; Nierlich, D. P. (1980-07-31). "Distinctive sequence of human mitochondrial ribosomal RNA genes". ...

https://en.wikipedia.org/wiki/28S_ribosomal_RNA

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 ...

https://en.wikipedia.org/wiki/De_novo_transcriptome_assembly

Many annotations of the sequences are based not on laboratory experiments, but on the results of sequence similarity searches ... The first nucleotide sequence database was created. Previously known as the European Molecular Biology Laboratory (EMBL) ... This can led to a transitive annotation problem because there may be several such annotation transfers by sequence similarity ... As a result, the sequences themselves, and especially the biological annotations attached to these sequences, may vary in ...

https://en.wikipedia.org/wiki/Sequence_database

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 ...

https://en.wikipedia.org/wiki/ZCCHC17

MolQuest is the most comprehensive, easy-to-use desktop application for sequence analysis and molecular biology data management ... Solovyev V, Salamov A. (2011). "Automatic Annotation of Microbial Genomes and Metagenomic Sequences". In R.W. Li (ed.). ... He is interested in genome structural and functional annotation and applying it for rational design of biological systems. ... The Fgenesb bacterial genome annotation pipeline based on Markov chain models was significantly superior to other approaches, ...

https://en.wikipedia.org/wiki/Victor_V._Solovyev

Molecular biology, Laboratory techniques, Molecular biology techniques, DNA sequencing). ... Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat. Methods. 2: 105-111 ... linker sequence, a short 5' sequence tag, a short 3' sequence tag, and a short 3' linker sequence. It was shown conceptually ... The sequences unique to the clone are now paired together. Depending on the next-generation sequencing technique, PET sequences ...

https://en.wikipedia.org/wiki/Paired-end_tag

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 ...

https://en.wikipedia.org/wiki/Computational_immunology

... annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences". Virology Journal. 4 ... v t e (GO template errors, RNA, Non-coding RNA, All stub articles, Molecular and cellular biology stubs). ... 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, ...

https://en.wikipedia.org/wiki/Hepatitis_B_virus_PRE_1151–1410

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 ...

https://en.wikipedia.org/wiki/Chromosome_2

The draft sequence of the 21 chromosomes enabled for the first time the annotation of 124,201 genes and comparative ... These sequences anchored to many molecular markers on genetic maps, provided a springboard for faster gene isolation, rapid ... At that time whole genome sequencing approaches did not yield any high quality sequence assemblies due to the extremely high ... "Wheat Genome Sequencing Gets Major Boost". International Wheat Genome Sequencing Consortium. 6 January 2016. Retrieved 15 March ...

https://en.wikipedia.org/wiki/Catherine_Feuillet

Xu, X.; Arnason, U. (1 May 1996). "A complete sequence of the mitochondrial genome of the western lowland gorilla". Molecular ... a mitochondrial genome database of fish with an accurate and automatic annotation pipeline". Molecular Biology and Evolution. ... In contrast to STR analysis, mtDNA sequencing uses Sanger sequencing. The known sequence and questioned sequence are both ... Human mitochondrial DNA was the first significant part of the human genome to be sequenced. This sequencing revealed that the ...

https://en.wikipedia.org/wiki/Mitochondrial_DNA

"A genome annotation-driven approach to cloning the human ORFeome". Genome Biology. 5 (10): R84. doi:10.1186/gb-2004-5-10-r84. ... Journal of Molecular Biology. 346 (5): 1275-86. doi:10.1016/j.jmb.2005.01.013. PMID 15713480. Weller S, Cajigas I, Morrell J, ... "The DNA sequence of human chromosome 22". Nature. 402 (6761): 489-95. Bibcode:1999Natur.402..489D. doi:10.1038/990031. PMID ...

https://en.wikipedia.org/wiki/PEX26

The gene ontology (GO) annotation for 165 plant species and GO enrichment analysis is available. The Molecular Signatures ... NASQAR (Nucleic Acid SeQuence Analysis Resource) is an open source, web-based platform for high-throughput sequencing data ... Exome sequences from women who had experienced SPTB were compared to those from females from the 1000 Genome Project, using a ... "NASQAR: Nucleic Acid SeQuence Analysis Resource". Yu G, Wang LG, Han Y, He QY (May 2012). "clusterProfiler: an R package for ...

https://en.wikipedia.org/wiki/Gene_set_enrichment_analysis

... isolation and mapping of 21 new genes using the expressed sequence tags database". Human Molecular Genetics. 5 (10): 1649-55. ... Gardiner K, Slavov D, Bechtel L, Davisson M (Jun 2002). "Annotation of human chromosome 21 for relevance to Down syndrome: gene ...

https://en.wikipedia.org/wiki/ABCC13

He has studied repeated sequences in the DNA of mice and produced molecular maps of mouse chromosomes, which were used to ... He has been at the forefront of new approaches in mutagenesis and phenotyping for the functional annotation of the mouse genome ... He pioneered studies of repeated sequences in the mouse genome and the use of novel approaches to generate molecular maps of ... A particular focus has been the use of mouse models to elucidate the molecular basis of genetic deafness. With Karen Steel, he ...

https://en.wikipedia.org/wiki/Stephen_D._M._Brown

Molecular Psychiatry. 17 (1): 36-48. doi:10.1038/mp.2010.109. PMC 3252611. PMID 21042317. Mandrile G, Dubois A, Hoffman JD, ... Non-identity calculated based on (1-NCBI sequence identity). Figure 5: Divergence rate of C3orf70 with respect to Cytochrome C ... "a protein domain database for functional characterization and annotation". Nucleic Acids Res. Retrieved 2015-04-19. "dbSNP". ... The precursor protein has been predicted with a molecular weight of 27.8kdal and an isoelectric point of 4.67. With 33 serines ...

https://en.wikipedia.org/wiki/C3orf70

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 ...

https://en.wikipedia.org/wiki/Chromosome_1

2007). "Genome sequence of Aedes aegypti, a major arbovirus vector". Science. 316 (5832): 1718-23. Bibcode:2007Sci...316.1718N ... 2008). "Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase". Insect Molecular Biology. 17 (1 ... mainly genome annotation). Aedes aegypti Anopheles gambiae Culex quinquefasciatus Ixodes scapularis Pediculus humanus Rhodnius ... 2002). "The genome sequence of the malaria mosquito Anopheles gambiae". Science. 298 (5591): 129-49. Bibcode:2002Sci...298.. ...

https://en.wikipedia.org/wiki/VectorBase

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 ...

https://en.wikipedia.org/wiki/QIAGEN_Silicon_Valley

Promoter DNA sequences provide an enzyme binding site. The -10 sequence is TATAAT. -35 sequences are conserved on average, but ... ORegAnno - Open Regulatory Annotation Database Identifying a Protein Binding Sites on DNA molecule YouTube tutorial video ... Molecular Cell Biology. 16 (3): 155-166. doi:10.1038/nrm3951. PMC 4963239. PMID 25693131. Mikhaylichenko O, Bondarenko V, ... The sequence at -10 (the -10 element) has the consensus sequence TATAAT. The sequence at -35 (the -35 element) has the ...

https://en.wikipedia.org/wiki/Promoter_(genetics)

"Generation and annotation of the DNA sequences of human chromosomes 2 and 4". Nature. 434 (7034): 724-731. Bibcode:2005Natur. ... The molecular weight of the protein is 76.5 kilodaltons, and the isoelectric point is 5.47.The gene has 6 transcript splice ... It is also known by the aliases Family with Sequence Similarity 178, Member B, and HSPC234. In total there are 24 exons in the ... "Clustal Omega < Multiple Sequence Alignment < EMBL-EBI". www.ebi.ac.uk. Retrieved 2019-04-29. "ExPASy: SIB Bioinformatics ...

https://en.wikipedia.org/wiki/FAM178B

TTC39B is expected to have a molecular binding function as well as a role in lipid regulation; the phenotype as well as the ... "TTC39B, a comprehensive annotation of human, mouse, and worm genes with mRNAs or ESTsAceView". AceView. Retrieved 13 May 2013 ... "NetPhos 2.0 Server". Center for Biological Sequence Analysis. Retrieved 13 May 2013. "SUMOsp 2.0 - SUMOylation Site Prediction ... "TTC39A, a comprehensive annotation of human, mouse, and worm genes with mRNAs or ESTsAceView". AceView. Retrieved 13 May 2013 ...

https://en.wikipedia.org/wiki/Tetratricopeptide_repeat_protein_39B

With the human genome sequenced, the next step is the verification and functional annotation of all predicted genes and their ... Current Opinion in Molecular Therapeutics. 4 (3): 242-50. PMID 12139310. Zhang B, VerBerkmoes NC, Langston MA, Uberbacher E, ... The name is derived from shotgun sequencing of DNA which is itself named after the rapidly expanding, quasi-random firing ... This further challenges the identification of the peptide sequence by means of conventional database matching approaches. ...

https://en.wikipedia.org/wiki/Shotgun_proteomics

It contains sequence motifs, of which there is a strong similarity with other TAA heads. This indicates that there is a lot of ... In molecular biology, trimeric autotransporter adhesins (TAAs), are proteins found on the outer membrane of Gram-negative ... Szczesny P, Lupas A (2008). "Domain annotation of trimeric autotransporter adhesins--daTAA". Bioinformatics. 24 (10): 1251-6. ... The GIN domain is a head domain named after its sequence motif GIN (Glycine-Isoleucine-Asparagine) motif. It has an all-beta ...

https://en.wikipedia.org/wiki/Trimeric_autotransporter_adhesin

The relationship between sequence and annotation". Bioinformatics. 19 (10): 1275-1283. doi:10.1093/bioinformatics/btg153. PMID ... International Conference on Intelligent Systems for Molecular Biology. 6: 25-34. PMID 9783206. Field, D.; Garrity, G.; Gray, T ... Jupp, S.; Stevens, R.; Hoehndorf, R. (2012). "Logical Gene Ontology Annotations (GOAL): Exploring gene ontology annotations ... Yesilada, Yeliz (2005). Annotation and transformation of web pages to improve mobility for visually impaired users (Ph.D. ...

https://en.wikipedia.org/wiki/Robert_Stevens_(scientist)

Completed genome sequences allow every open reading frame (ORF), the part of a gene that is likely to contain the sequence for ... This method may help identify distantly related proteins and can be used to infer molecular functions. There are currently a ... has recently developed a wiki-based approach namely Open protein structure annotation network (TOPSAN) for annotating protein ... The gene sequence of the target protein can also be compared to a known sequence and structural information can then be ...

https://en.wikipedia.org/wiki/Structural_genomics

Zhou J, Xu Y, Lin S, Guo Y, Deng W, Zhang Y, Guo A, Xue Y (January 2018). "iUUCD 2.0: an update with rich annotations for ... Molecular Cell Biology. 16 (1): 30-44. doi:10.1038/nrm3919. PMC 5131867. PMID 25531226. Shpilka T, Mizushima N, Elazar Z (May ... UBLs that are capable of conjugation (sometimes known as Type I) have a characteristic sequence motif consisting of one to two ... Molecular Cell Biology. 6 (8): 599-609. doi:10.1038/nrm1700. PMID 16064136. S2CID 7373421. Goldstein G, Scheid M, Hammerling U ...

https://en.wikipedia.org/wiki/Ubiquitin-like_protein

Swiss-Prot is a curated protein sequence database which strives to provide a high level of annotation (such as the description ... Hirata R, Ohsumk Y, Nakano A, Kawasaki H, Suzuki K, Anraku Y (April 1990). "Molecular structure of a gene, VMA1, encoding the ... Recognition sequence: Sequence of DNA recognized by the enzyme. The enzyme is specifically bound to this sequence. Cut: Cutting ... Both the recognition sequence and the cutting site match usually, but sometimes the cutting site can be dozens of nucleotides ...

https://en.wikipedia.org/wiki/List_of_homing_endonuclease_cutting_sites

A molecular test that detects the presence of cell-associated PCA3 mRNA in fluid obtained from the prostate and first-void ... Retracted, see doi:10.1371/annotation/7e2efc01-2e9b-4e9b-aef0-87ab0e4e4732) Arnst C (2007-06-13). "A Gender Gap in Cancer". ... Tran K, McGill S. Treatment Sequences of Androgen Receptor-Targeted Agents for Prostate Cancer [Internet]. Ottawa (ON): ... April 2016). "Low-Molecular-Weight Protein Tyrosine Phosphatase Predicts Prostate Cancer Outcome by Increasing the Metastatic ...

https://en.wikipedia.org/wiki/Prostate_cancer

"Molecular Diet Analysis of Two African Free-Tailed Bats (Molossidae) Using High Throughput Sequencing". PLOS ONE. 6 (6): e21441 ... and Annotation of Four DNA Markers". PLOS ONE. 11 (6): 1-16. Bibcode:2016PLoSO..1157505F. doi:10.1371/journal.pone.0157505. ... The purified DNA is then amplified for a specific gene target so it can be sequenced and categorised based on its sequence. ... However, assignment of the eDNA sequences to known organisms is done via comparison with reference sequences (or barcodes) made ...

https://en.wikipedia.org/wiki/Environmental_DNA

DNA sequences and genotypes Molecular expression data often generated using arrays, RNA-seq, epigenomic, proteomic, metabolomic ... GeneNetwork includes annotation files for several RNA profiling platforms (Affymetrix, Illumina, and Agilent). RNA-seq and ... This resource is used to study gene regulatory networks that link DNA sequence differences to corresponding differences in gene ... locus mapping and causal models of the linkage between sequence differences and phenotype differences Traits and molecular ...

https://en.wikipedia.org/wiki/GeneNetwork

... primarily focused on molecular biology and sequence analysis. NDVis is an interactive data visualization and analysis tool for ... text mining techniques for network validation and annotation, and Web services-based workflow techniques. BioSPICE is a ...

https://en.wikipedia.org/wiki/List_of_NetBeans-based_software

While the molecular target for these non-genomic effects of nuclear receptors has not been conclusively demonstrated, it has ... The placement of C. elegans nhr-1 (Q21878) is disputed: although most sources place it as NR1K1, manual annotation at WormBase ... The A-B domain is highly variable in sequence between various nuclear receptors. (C) DNA-binding domain (DBD): Highly conserved ... A molecular mechanism for non-genomic signaling through the nuclear thyroid hormone receptor TRβ involves the ...

https://en.wikipedia.org/wiki/Nuclear_receptor

The package was also integrated with the RCSB PDB web application and added protein modification annotations to the sequence ... Also, the previous data models for macro-molecular structures have been adapted to more closely represent the mmCIF data model ... For Multiple Sequence Alignment, any of the methods discussed above can be used to progressively perform a multiple sequence ... parsing and manipulation Manipulating individual sequences Searching for similar sequences Creating and manipulating sequence ...

https://en.wikipedia.org/wiki/BioJava

2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315-21. Bibcode:2006Natur.441.. ... 2002). "Human peptidylarginine deiminase type II: molecular cloning, gene organization, and expression in human skin". Arch. ... 1999). "Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones ... 2001). "The sequence of the human genome". Science. 291 (5507): 1304-51. Bibcode:2001Sci...291.1304V. doi:10.1126/science. ...

https://en.wikipedia.org/wiki/PADI2

The Qatar Genome Programme aims to sequence the genomes of 350,000 inhabitants of Qatar. Supported by the Sidra Medical and ... Genetic epidemiological studies by integrating genomic data and variant annotations are also underway for autoinflammatory ... Molecular Genetics and Genomics. 293 (4): 919-929. doi:10.1007/s00438-018-1431-8. ISSN 1617-4623. PMID 29557500. S2CID 3945453 ... Albagha, Thareja; Suhre, Al-Sarraj (2021). "Whole genome sequencing in the Middle Eastern Qatari population identifies genetic ...

https://en.wikipedia.org/wiki/Qatar_Genome_Programme

2004). "The sequence and analysis of duplication-rich human chromosome 16" (PDF). Nature. 432 (7020): 988-94. Bibcode:2004Natur ... Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome ... 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 57 member B FBRS: Probably fibrosin-1 long transcript protein FOXC2-AS1: encoding protein FOXC2 ...

https://en.wikipedia.org/wiki/Chromosome_16

Thus, the annotation of new sequences is mostly by prediction through computational methods, as these types of annotation can ... Whereas homology-based methods can often be used to identify molecular functions of a protein, context-based approaches can be ... Proteins of similar sequence are usually homologous and thus have a similar function. Hence proteins in a newly sequenced ... There is no hard sequence-similarity threshold for "safe" function prediction; many proteins of barely detectable sequence ...

https://en.wikipedia.org/wiki/Protein_function_prediction

Journal of Molecular Biology. Computation Resources for Molecular Biology. 430 (15): 2237-2243. doi:10.1016/j.jmb.2017.12.007. ... Wright ES (2015). "Using DECIPHER v2.0 to Analyze Big Biological Sequence Data in R". The R Journal. 8 (1): 352-359. doi: ... Jorda, Julien; Kajava, Andrey V. (2009-10-15). "T-REKS: identification of Tandem REpeats in sequences with a K-meanS based ... Richard, François D.; Kajava, Andrey V. (2014-06-01). "TRDistiller: A rapid filter for enrichment of sequence datasets with ...

https://en.wikipedia.org/wiki/List_of_protein_tandem_repeat_annotation_software

The DNA sequence is 89,840bp long. CCDC138 is the only established common alias. No paralogs of CCDC138 have been identified. ... The CCDC138 protein is predated to have a molecular weight of 76.2Kda and an isoelectric point of 8.614. Compositional analysis ... "AceView: Gene:CCDC138, a Comprehensive Annotation of Human, Mouse and Worm Genes with mRNAs or ESTs". Retrieved 30 March 2014 ... The majority of the sequence are coiled-coils and alpha helixes. There are no predicted 3° and 4° Structures for the CCDC138 ...

https://en.wikipedia.org/wiki/CCDC138

A re-annotation was made in 2003. Venkateswaran, K.; Moser, D. P.; Dollhopf, M. E.; Lies, D. P.; Saffarini, D. A.; MacGregor, B ... In 2002, its genomic sequence was published. It has a 4.9Mb circular chromosome that is predicted to encode 4,758 protein open ... Molecular Microbiology. 30 (2): 285-293. doi:10.1046/j.1365-2958.1998.01061.x. ISSN 0950-382X. PMID 9791174. S2CID 26631504. ... 2002). "Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis". Nature Biotechnology. 20 (11 ...

https://en.wikipedia.org/wiki/Shewanella_oneidensis

2005). "Generation and annotation of the DNA sequences of human chromosomes 2 and 4". Nature. 434 (7034): 724-31. Bibcode: ... HADHB is a functional molecular target of ERα in the mitochondria, and the interaction may play an important role in the ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... 2009). "Clinical and molecular aspects of Japanese patients with mitochondrial trifunctional protein deficiency". Mol. Genet. ...

https://en.wikipedia.org/wiki/HADHB

Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome ... Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2. Genome ... October 2003). "The DNA sequence and analysis of human chromosome 6". Nature. 425 (6960): 805-11. Bibcode:2003Natur.425..805M. ... signal sequence receptor subunit 1 (6p24.3) TCF19: transcription factor 19 (6p21.33) TCP11: t-complex 11 (6p21.31) TJAP1: tight ...

https://en.wikipedia.org/wiki/Chromosome_6

The histone mark acetylation can be detected in a variety of ways: 1. Chromatin Immunoprecipitation Sequencing (ChIP-sequencing ... Molecular Cell Biology. 8 (12): 983-94. doi:10.1038/nrm2298. PMC 4690530. PMID 18037899. Kouzarides T (February 2007). " ... This additional level of annotation allows for a deeper understanding of cell specific gene regulation. ... Well positioned nucleosomes are seen to have enrichment of sequences. 3. Assay for transposase accessible chromatin sequencing ...

https://en.wikipedia.org/wiki/H4K8ac

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... ... Complete DNA sequence plasmid comparisons. Bands of color indicate homology between sequences. Red lines show sequence... ... Complete Sequence and Molecular Epidemiology of IncK Epidemic Plasmid Encoding blaCTX-M-14 On This Page ...

http://www.cdc.gov/eid/content/17/4/645.htm

Molecular Sequence Annotation * Software* ... The new GO annotation and orthology data are available for ... We have computed Gene Ontology (GO) annotations for all species, greatly enhancing the GO annotation data gathered from UniProt ... Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses Nucleic ...

https://pubmed.ncbi.nlm.nih.gov/34747465/

We developed a new approach to address this challenge, combining long-range PCR and nanopore sequencing with a novel ... a Annotation and read count for novel exonic sequences within CACNA1C. Red arrows indicate exons that have been validated ( ... To limit the impact of sequencing errors on transcript annotations, we filtered the identified transcripts retaining only those ... Our study highlights the power of long-read sequencing for the annotation and characterisation of alternatively spliced ...

https://www.nature.com/articles/s41380-019-0583-1?error=cookies_not_supported&code=d6b2d12c-901f-4736-8fd2-c4b55ea74f54

Genome project design, DNA sequencing methods and annotation. Molecular evolution. Phylogenetic inference methods. Applications ... Molecular structure and chemical bonding using the VSEOR model. Nomenclature of inorganic ions and compounds. Classification of ... Molecular origin of Mendelian and multifactorial diseases. The use of polymorphisms, gene mapping, linkage and association ... Practical: Molecular structure (model building), synthesis and properties of simple organic compounds. ...

https://www.up.ac.za/faculty-of-education/yearbooks/2018/SCI-faculty/UD-programmes/view/02133396/lg/Gallery

Groth, D.; Hartmann, S.; Panopoulou, G.; Poustka, A. J.; Hennig, S.: GOblet: annotation of anonymous sequence data with Gene ... Groth, D.; Lehrach, H.; Hennig, S.: GOblet: a platform for Gene Ontology annotation of anonymous sequence data. Nucleic Acids ... Hennig, S.; Groth, D.; Lehrach, H.: Automated Gene Ontology annotation for anonymous sequence data. Nucleic Acids Research 31 ( ... The DNA sequence, annotation and analysis of human chromosome 3. Nature 440 (7088), pp. 1194 - 1198 (2006) ...

https://www.molgen.mpg.de/publication-search/3450192?person=%2Fpersons%2Fresource%2Fpersons50200

Molecular Sequence Annotation. dc.title. Meta-analysis of Immunochip data of four autoimmune diseases reveals novel single- ... Cell-specific functional annotations and biological pathway enrichment analyses suggested that pleiotropic variants may act by ... thus shedding light on common molecular mechanisms of disease and suggesting novel drug targets that could be explored for the ...

https://www.repository.cam.ac.uk/handle/1810/289619?show=full

Molecular Sequence Annotation 29% * Defining the pig microglial transcriptome reveals its core signature, regional ...

https://www.research.ed.ac.uk/en/persons/barbara-shih/publications/?ordering=type&descending=false

Genome sequencing and annotation of a Campylobacter coli strain isolated from milk with multidrug resistance. In: Genomics Data ... Genome sequencing and annotation of a Campylobacter coli strain isolated from milk with multidrug resistance. Genomics Data. ... Genome sequencing and annotation of a Campylobacter coli strain isolated from milk with multidrug resistance. / Liu, Kun C.; ... Liu, K. C., Jinneman, K. C., Neal-McKinney, J., Wu, W. H., & Rice, D. H. (2016). Genome sequencing and annotation of a ...

https://jhu.pure.elsevier.com/en/publications/genome-sequencing-and-annotation-of-a-campylobacter-coli-strain-i

We obtained 2,486 expressed sequence tags (ESTs) from 2,586 clones derived from the cDNA library of desiccated P. murrayi. The ... had no significant match to any sequences in the current databases. The 1,387 unique transcripts were functionally classified ... Annotation based on most significant BLAST alignment for each cluster.. *₤Percentage based on total number of high quality ... From: Desiccation survival in an Antarctic nematode: molecular analysis using expressed sequenced tags ...

https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-10-69/tables/3

Molecular marker based taxonomical annotation using Mitochondrial COI gene sequencing confirmed the identity of the specimen. ...

https://bioone.org/journals/zoosystema/volume-40/issue-1/zoosystema2018v40a4/First-record-and-DNA-Barcoding-of-Oman-cownose-ray-Rhinoptera/10.5252/zoosystema2018v40a4.short

The molecular sequence of this clone aligns with the gene accession number as a point of reference only. However, individual ... OTI Annotation. This clone was engineered to express the complete ORF with an expression tag. Expression varies depending on ... Sequence Data. ORF Nucleotide Sequence (showhide) >RC204239 ORF sequence. Red=Cloning site Blue=ORF Green=Tags(s). ... Protein Sequence (showhide) >RC204239 protein sequence. Red=Cloning site Green=Tags(s). ...

https://www.origene.com/catalog/cdna-clones/expression-plasmids/rc204239/shmt2-nm_005412-human-tagged-orf-clone

Samples are analyzed using whole genome sequencing (WGS) and comparative phylogenomic methods. These results are communicated ... The Molecular Core accepts samples from the NTM Culture, Biorepository, and Coordinating Core. ... MycoBASE: expanding the functional annotation coverage of mycobacterial genomes.. Benjamin J. Garcia, Gargi Datta, Rebecca M. ... Genome Sequence of an Epidemic Isolate of Mycobacterium abscessus subsp. bolletii from Rio de Janeiro, Brazil.. Rebecca M. ...

https://www.nationaljewish.org/research-science/cocfrdp/core-services/molecular-core/cfntm

Disease (disease genes where sequence variants are found in this domain). * SwissProt sequences and OMIM curated human diseases ... Locating the mutated residues on the yeast cofilin molecular structure allowed several important conclusions to be drawn. First ... Sequences derived from large peptides mapping near the amino terminal show homology to the amino-terminal actin-binding site of ... Instead, the sequence of a domain located near the center of the filamin molecule (tryptic 100-kDa peptide, T100) shows ...

https://smart.embl.de/smart/do_annotation.pl?DOMAIN=CH&START=18&END=120&E_VALUE=2.38e-26&TYPE=SMART&BLAST=QQNTFTRWCNEHLKCVNKRIGNLQTDLSDGLRLIALLEVLSQKRMHHKYHQRPTFRQMKLENVSVALEFLDHESIKLVSIDSKAIVDGNLKLILGLVWTLILH

Purification and molecular cloning of the "A" chain of a rat heteromeric CCAAT-binding protein. Sequence identity with the ... Portions of CBF-A and CBF-B have a high degree of amino acid sequence identity to segments of the HAP3 and HAP2 subunits of a ... DNA sequence analysis of a representative cDNA clone revealed the presence of an open reading frame of 207 amino acids coding ... Amino acid sequences of two of these tryptic peptides were used to synthesize oligonucleotide primers. The primers served to ...

http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=CBF&BLAST=DUMMY

Analyse large molecular datasets such as raw microarray data and genomic sequence data for clinical or basic research purposes. ... Compile data for use in activities such as gene expression profiling, genome annotation, and structural bioinformatics. ... Perform analysis on next generation sequencing data including genetic variant calling, gene expression and others (added ... Perform analysis on next generation sequencing data including genetic variant calling, gene expression and others. ...

https://www.timeshighereducation.com/unijobs/listing/309350/research-fellow-bioinformatician-department-of-obstetrics-and-gynaecology-/?LinkSource=SimilarJobPlatform

The sequence-structure relationship of three new subfamilies was examined by molecular modelling. I provide structural models ... The domain within your query sequence starts at position 118 and ends at position 141; the E-value for the LRR domain shown ... In recentyears, a number of diverse plant proteins with low sequence similarity toBet v 1 was identified. In addition, ... Novel Molecular Architecture of YopM-a Leucine-rich Effector Protein from Yersinia pestis. ...

https://smart.embl.de/smart/do_annotation.pl?DOMAIN=LRR&START=118&END=141&E_VALUE=1.71e1&TYPE=SMART&BLAST=LNELKQLFLCQNKILQLNPDTFVP

4. Molecular Biology (Splice-junction Gene Sequences): Primate splice-junction gene sequences (DNA) with associated imperfect ... 3. Anticancer peptides: Peptides with experimental annotations on their anticancer action on breast and lung cancer cells. ... 1. Molecular Biology (Promoter Gene Sequences): E. Coli promoter gene sequences (DNA) with partial domain theory ... 2. Molecular Biology (Protein Secondary Structure): From CMU connectionist bench repository; Classifies secondary structure of ...

https://archive.ics.uci.edu/ml/datasets.php?format=&task=&att=&area=life&numAtt=&numIns=&type=seq&sort=instUp&view=list

Sequence Annotation. View plasmid maps, automatically annotate vectors, find restriction sites; digest, ligate, and perform ... Molecular Cloning. View plasmid maps, annotate vectors, find restriction sites; digest, ligate, and perform Golden Gate, Gibson ... I first got it to make alignment and trees of my sequences and it works well for those purposes. But it was a real lifesaver a ... may be in the form of multiple alignments or a a GenBank BLAST file with annotations superimposed on top of a protein sequence ...

https://www.geneious.com/features/vector-nti-importer/

10,000 expressed sequence tags (ESTs) corresponding to 8149 unique sequences from this species. A direct comparison with EST ... Molecular Biology and Evolution (MBE). ISSN 0737-4038. doi: 10.1093/molbev/msx075. Show summary The innovation of the eukaryote ... genome annotation). ... Genome sequencing and de novo assembly of the giant unicellular ... Biosynthesis and Molecular Genetics of Polyketides in Marine Dinoflagellates. Marine Drugs. ISSN 1660-3397. 8(4), p. 1011-1048. ...

https://www.mn.uio.no/ibv/english/people/aca/rjsorr/

A Next-Generation Sequencing-Based Molecular Approach to Characterize a Tick Vector in Lyme Disease. Madugundu, A. K., ... A functional annotation of subproteomes in human plasma. Ping, P., Vondriska, T. M., Creighton, C. J., Gandhi, T. K. B., Yang, ... Bellad, A., Bandari, A. K., Pandey, A., Girimaji, S. C. & Muthusamy, B., Sep 1 2020, In: Journal of Molecular Neuroscience. 70 ... Antitumor activity and molecular effects of the novel heat shock protein 90 inhibitor, IPI-504, in pancreatic cancer. Song, D. ...

https://mayoclinic.pure.elsevier.com/en/persons/akhilesh-pandey/publications/?ordering=type&descending=false

... sequences and swine SSC 10.2 annotation. In the PacBio dataset, a total of 1,093,282 high-quality FLNC sequences covered ... Molecular Breeding 2009, 25(4):553-570.. *Li F, Fan G, Lu C, Xiao G, Zou C, Kohel RJ, Ma Z, Shang H, Ma X, Wu J et al: Genome ... under DS and RD stress at the seedling stage using single-molecule real-time sequencing and RNA-sequencing. Gene Ontology (GO) ... Each SMRT cell line was sequenced using P6 C4 reagent on the PacBio RS II platform with 4 h sequencing movies. ...

https://www.researchsquare.com/article/rs-11018/v4

This module can also suggest the AMP family to which the query sequence is likely to belong and its potential function. ANTIMIC ... The ANTIMIC database has keyword search option and has integrated tools to aid the analysis at molecular level. The integrated ... and enriched in annotation. ... BLAST module for the analysis of similarity of query sequence ...

https://www.iscb.org/cms_addon/conferences/ismb2003/posters/manishaATlit.org.sg_344.html

... a fast and simple web server for genome scale functional annotation of plant sequence data. Plant Cell Environment 37 (5), pp. ...

https://www.mpimp-golm.mpg.de/publication-search/1358655?person=%2Fpersons%2Fresource%2Fpersons97313

These databases include DNA and protein sequences and structures, genome annotation, gene expression information, molecular ... and the detailed understanding of the molecular apparatus behind cellular mechanisms of sequence information. By exploiting ... Pathway annotations are authored by expert biologists, in collaboration with Reactome editorial staff and cross-referenced to ... In the last decade, the Center for Biological Sequence Analysis has produced a large number of computational methods, which are ...

https://www.re3data.org/search?query=&databaseAccess%5B%5D=open

Peter Mac has designed a Molecular Genomics Diagnostic Reporting Package (PathOS) that uses cutting edge bioinformatics tools, ... Short read sequence typing (SRST): multi-locus sequence types from short reads, M Inouye, TC Conway, J Zobel, KE Holt, BMC ... PathOS enables bioinformatics filtering, classification of variants, annotation, curation and clinical reporting all in a ... Molecular diagnostic software. Peter Mac has designed a Molecular Genomics Diagnostic Reporting Package (PathOS) that uses ...

https://www.petermac.org/about/signature-centres/centre-clinical-cancer-genomics/molecular-diagnostic-software

Whole Genome Sequencing, Assembly, and Annotation of Odontesthes Bonariensis (Pejerrey), a Fish with Temperature-dependent Sex ... The Application of Molecular Biological Technologies in Prenatal Diagnosis Tze Kin LAU, The Chinese Fetal Medicine Foundation ... See Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum Paper based on PhD thesis work of ... uBiome-Sequencing the Human Microbiome Using Citizen Science Zachary Apte, uBiome. *Crowdsourcing Analyses of the Emergent ...

https://phylogenomics.blogspot.com/2014/01/kudos-to-doe-jgi-for-organizing.html

GBrowse (Generic Genome Browser), a part of GMOD is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. (open-bio.org)
The knowledge of mitochondrial genomes has been widely useful for the studies on molecular evolution, phylogenetics and population genetics. (biomedcentral.com)
Although, providing the massive amount of data by recent genome sequencing projects but many of these genomes are still not fully annotated as well as consist of genes/proteins with unknown function and structure. (avensonline.org)
Despite the increasing accessibility of high-throughput sequencing, obtaining high-quality genomic data on non-model organisms without proximate well-assembled and annotated genomes remains challenging. (datadryad.org)
UniProt provides proteomes for species with completely sequenced genomes. (weinberginternational.com)
A. 46-Way Sequence Conservation: based on multiple sequence alignment scores, at the nucleotide level, of 46 vertebrate genomes compared with the human genome. (sanger.ac.uk)
Cardiocondyla obscurior has the smallest of the sequenced ant genomes and its structure suggests a fundamental role of transposable elements (TEs) in adaptive evolution. (wurmlab.com)
We sequenced the whole genomes of 21 N. gonorrhoeae isolates collected in 2013-2014 by ARSP. (who.int)
The annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. (gob.ar)
Our revolutionary sequencing technologies combine the completeness of long reads with the accuracy of short reads to provide the most comprehensive view of genomes, transcriptomes, and epigenomes. (pacb.com)

Pathogen Surveillance and Characterization using Whole Genome Sequencing: The Colorado Cystic Fibrosis Research and Development Program - Molecular and Genomics Core. (nationaljewish.org)
Peter Mac has designed a Molecular Genomics Diagnostic Reporting Package (PathOS) that uses cutting edge bioinformatics tools, federation of databases and a clinical information exchange platform to provide the clinician with a comprehensive account of the patient's genomic landscape, a list of "actionable" mutations (e.g. mutations that can be specifically targeted using so-called designer drugs). (petermac.org)
The specific application areas of our research include genome analysis and comparison, cDNA-to-genome alignment, gene and alternative splicing annotation, RNA editing, microbial comparative genomics, miRNA genomics and computational vaccine design. (hopkinsmedicine.org)
Bio-ontologies provide a structured, controlled vocabulary through which data-especially those gathered through sequencing and genomics, but increasingly also those resulting from other types of research-can be classified in a form that can be stored in and retrieved from online databases. (semanticscholar.org)
Computational Proteomics: Filtering and indexing sequence databases, Peptide quantification and identification, Genome annotations via mass spectrometry, Identification of post-translational modifications, Structural genomics via mass spectrometry, Protein-protein interactions, Computational approaches to analysis of large scale Mass spectrometry data, Exploration and visualization of proteomic data, Data models and integration for proteomics and genomics, Querying and retrieval of proteomics and genomics data etc. (wikicfp.com)
The samples were sequenced on an Illumina Hiseq 4000 at the Beijing Genomics Institute, China. (globalrust.org)

We have computed Gene Ontology (GO) annotations for all species, greatly enhancing the GO annotation data gathered from UniProt with more than a ten-fold increase in the number of GO-annotated genes. (nih.gov)
This is due to the limited availability of high-quality, post-mortem human tissue and to technical limitations associated with standard approaches: most rely on short-read RNA-Seq and the reconstruction of fragmented sequences making the disambiguation of full-length transcripts difficult, particularly for large and complex genes. (nature.com)
Blavier told BioInform that beta testers have praised the "comprehensiveness" of Alamut HT's annotations, which include information on the effects of variants on human genes, information on SNPs, and missense and splicing predictions. (genomeweb.com)
Compilation of tRNA sequences and sequences of tRNA genes. (vldb.org)
To identify genes and miRNAs involved in drought stress responses in S. tonkinensis , both mRNA and small RNA sequencing was performed in root samples under control, mild drought, and severe drought conditions. (biomedcentral.com)
RNA was sequenced and 63 wheat genes were identified that showed varying expression in response to the six races. (globalrust.org)
Using hybrid capture, the genes of interest are enriched and sequenced on the Illumina HiSeq 2500 or MiSeq sequencers followed by variant detection and functional and clinical annotation for the generation of a clinical report. (jax.org)
Signatures come in two flavors: Unsigned - A set of genes that have some common annotation. (nsmalondon.com)
Click "Phenotype Details" to view all phenotype annotations and evidence for this locus as well as phenotypes it shares with other genes. (yeastgenome.org)
Interaction annotations are curated by BioGRID and include physical or genetic interactions observed between at least two genes. (yeastgenome.org)
The most visible biological application today is the Gene Ontology project [ 1 ], which provides a controlled vocabulary for cross-species comparisons of genes and gene products that are associated with biological processes, molecular functions, and cellular components. (biomedcentral.com)
Based on phenotypic characterization, expression analysis and ChIP-seq of Hox genes during in vitro MN differentiation, we plan to identify the enhancer structure at Hox binding sites and to establish the minimal set of cofactors and molecular logic required for Hox gene activity in MNs. (nyu.edu)
This is achieved through mechanistic studies of functionally important epigenetic "driver" genes and molecular pathways altered by specific cancer risk agents and by the application of cutting-edge epigenomics in conjunction with unique biospecimens from population-based cohorts (Figure 1). (who.int)

Then we performed full-length transcriptome sequencing of drought-resistant variety (Z141) and drought-sensitive variety (NY-17) under DS and RD stress at the seedling stage using single-molecule real-time sequencing and RNA-sequencing. (researchsquare.com)
Illumina high-throughput sequencing of the whole body transcriptome of D. reticulatum generated a total of 5.9 billion raw paired-end reads. (oregonstate.edu)
Our results provide comprehensive transcriptome data of the gray garden slug, with a more detailed focus on the rich repertoire of putative neuropeptide sequences, laying the foundation for molecular studies in this terrestrial slug pest. (oregonstate.edu)
Maudhoo, M. D., Madison, J. D, and Norgren, R. B. (2015) De novo assembly of the chimpanzee transcriptome from NextGen mRNA sequences . (unmc.edu)
Gene set variation analysis (GSVA) R package was used to estimate the signaling pathways based on transcriptome sequencing data of each sample. (nsmalondon.com)
These features also further accelerated PacBio's Iso-Seq™ application to deliver whole-transcriptome sequencing of full-length cDNA transcripts to distinguish between isoforms for genome annotation, as well as gene discovery. (pacb.com)

It is so easy to search and then import GenBank files along with their annotations. (geneious.com)
This may be in the form of multiple alignments or a a GenBank BLAST file with annotations superimposed on top of a protein sequence with all of the predicted protein properties displayed. (geneious.com)
BioSQL is a generic unifying schema for storing sequences from different sources, for instance Genbank or Swissprot. (open-bio.org)
VADR: validation and annotation of virus sequence submissions to GenBank. (cdc.gov)
All genome sequence information is available on GenBank ( https://www.ncbi.nlm.nih.gov/genbank/ ), BioProject PRJNA759631. (jgenomics.com)

Dr Thomas Conway - Bioinformatics Researcher & Bioinformatician - Research interests in bringing together insights from theoretical computer science, statistics, and biology to unlock the potential of high throughput sequencing for for both research, and clinical practice. (petermac.org)
and the Institute of Genetics and Molecular and Cellular Biology in Strasbourg, France. (genomeweb.com)
The Molecular Biology Database Collection: 2005 update. (vldb.org)
Omics sciences are able to produce, with the modern high-throughput techniques of analytic chemistry and molecular biology, a huge quantity of data. (hindawi.com)
Knowing protein function is crucial to advance molecular and medical biology, yet experimental function annotations through the Gene Ontology (GO) exist for fewer than 0.5% of all known proteins. (rostlab.org)
The laboratory mouse represents an important model system for understanding human biology and the molecular basis of human diseases. (encodeproject.org)
BioRuby is a collection of open-source Ruby code, comprising classes for computational molecular biology and bioinformatics . (open-bio.org)
It contains classes for DNA and protein sequence analysis , sequence alignment , biological database parsing, structural biology and other bioinformatics tasks. (open-bio.org)
EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. (open-bio.org)

The new GO annotation and orthology data are available for searching in HymenopteraMine, and as bulk file downloads. (nih.gov)
GOblet: annotation of anonymous sequence data with Gene Ontology and pathway terms. (mpg.de)
Experience in the creation of data algorithms and specialised computer software to identify and classify components of a biological system, such as DNA sequences. (timeshighereducation.com)
Perform analysis on next generation sequencing data including genetic variant calling, gene expression and others. (timeshighereducation.com)
Compile data for use in activities such as gene expression profiling, genome annotation, and structural bioinformatics. (timeshighereducation.com)
Analyse large molecular datasets such as raw microarray data and genomic sequence data for clinical or basic research purposes. (timeshighereducation.com)
RESULTS: Structural comparisons ofrepresentative members of already known protein families structurallyrelated to Bet v 1 with all entries of the Protein Data Bank yielded 47structures with non-identical sequences. (embl.de)
Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. (mpg.de)
Interactive Biosoftware has released a new version of its flagship Alamut mutation analysis software designed to identify variants in next-generation sequence data. (genomeweb.com)
Andre Blavier, Interactive's founder and CEO, explained to BioInform this week that Alamut HT incorporates some of the same capabilities of its predecessor, but is intended for use in analysis pipelines to detect variants in whole-genome and whole-exome sequence data rather than as a front-end tool for inspecting mutations. (genomeweb.com)
Alamut HT "has a pretty rich database of variant annotation and it is able to get us the data in a format that we are then able to apply our own algorithms on," he told BioInform . (genomeweb.com)
Meanwhile, a company like BioBase, which provides some of the annotation data used in Alamut and Alamut HT, isn't a threat because its offerings aren't designed for use within analysis pipelines, Blavier said. (genomeweb.com)
The first mitochondrial genome from the Agrolimacidae family provides valuable molecular data for taxonomical identification and further evolutionary studies of terrestrial slugs. (oregonstate.edu)
We work to develop computational methods for analyzing large-scale sequencing data to help characterize molecular mechanisms of diseases. (hopkinsmedicine.org)
NGS enables large-scale B-cell receptor (BCR) repertoire profiling and the annotation of molecular-level immunogenetic data including V/D/J gene usage, combinatorial rearrangement, junctional diversity, and somatic mutation-all of which reveal the complex mechanisms underlying B-cell diversification and adaptive immune responses. (frontiersin.org)
We propose a strategy that incorporates genomic sequence data and metabolite profiles into modeling approaches to arrive at improved gene annotations and more complete genome -scale metabolic networks. (rsc.org)
We carefully evaluate our strategy on the well-studied metabolic network of Escherichia coli , demonstrating how the predictions can be improved by incorporating sequence data. (rsc.org)
The Research Molecular Pathology Laboratory provides targeted DNA sequencing and data interpretation, gene expression assays, tissue-based digital spatial profiling, circulating tumor cell isolation , digital PCR, and RNA in situ hybridization services. (cityofhope.org)
Biological knowledge is inherently complex and so cannot readily be integrated into existing databases of molecular (for example, sequence) data. (semanticscholar.org)
A DAS client merges data from two annotation servers if they both use segments having the same global reference name. (open-bio.org)
The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. (open-bio.org)
We enriched the Culex mt genome data and provided a reference basis for further Culex mt genome sequencing and analyses. (biomedcentral.com)
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record. (bvsalud.org)
Background: Differential expression (DE) analysis of RNA-seq data typically depends on gene annotations. (elsevier.com)
Next, a single-cell sequencing analysis on UM patients from the GEO data was used to characterize the lipid metabolism in TME and the role of MGLL in UM. (bvsalud.org)
Torrent Suite software was used for next generation sequencing raw data processing and variant calling. (who.int)
Gray triangles = other expression annotations only (e.g. absence of expression or data from mutants). (jax.org)
These ontologies standardize and expand current terminology for fetal and adult lungs, providing a qualitative framework for data annotation, retrieval, and integration across a wide variety of datasets in the BREATH database. (biomedcentral.com)
Sequence similarity was brought in through Protein Data Bank and non-redundant database using BLASTp program of NCBI and a search for templates revealed that yjaB shares 97% homology to a protein of Escherichia coli, indicating this protein is evolutionary conserved and was found with acetyltransfarase. (avensonline.org)
Skimming off-target sequence data from the same enriched libraries of Coelaturini from the Malawi Basin, we reconstructed the maternally-inherited mitogenome, which displays the gene order inferred for the most recent common ancestor of Unionidae. (datadryad.org)
Raw sequencing data are available at NCBI under BioProject PRJNA893605. (datadryad.org)
The multilocus sequence type, multiantigen sequence type, presence of determinants of antimicrobial resistance and relatedness among the isolates were all derived from the sequence data. (who.int)
With 18 Gb of sequencing data at 65x genome coverage and read length N50 at 16,485 bp, this yielded an HGAP genome assembly containing 625 contigs at a contig N50 of 2.39 Mb. (pacb.com)

Cell-specific functional annotations and biological pathway enrichment analyses suggested that pleiotropic variants may act by deregulating gene expression in different subsets of T cells, especially Th17 and regulatory T cells. (cam.ac.uk)
In recent years, genome sequencing projects have enormously increased our molecular understanding of biological capabilities of organisms. (biomedcentral.com)
Unique identifiers that are associated with each concept in biological ontologies (bio-ontologies) can be used for linking to and querying molecular databases. (semanticscholar.org)
It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of biological sequences and 3D structures. (open-bio.org)
Collaborative ontology project for the definition of sequence features used in biological sequence annotation. (open-bio.org)
GO Annotations consist of four mandatory components: a gene product, a term from one of the three Gene Ontology (GO) controlled vocabularies ( Molecular Function , Biological Process , and Cellular Component ), a reference, and an evidence code. (yeastgenome.org)
selleck kinase inhibitor Molecular methods in biological systems. (mdm2signaling.com)

Samples are analyzed using whole genome sequencing (WGS) and comparative phylogenomic methods. (nationaljewish.org)
Partners Healthcare evaluated the product as one of several variant-annotation methods it is considering as part of its effort to launch a whole-genome sequencing service later this year, Matthew Lebo, assistant laboratory director for PCPGM's molecular medicine lab, told BioInform this week. (genomeweb.com)
Computational methods bridge this sequence-annotation gap typically through homology-based annotation transfer by identifying sequence-similar proteins with known function or through prediction methods using evolutionary information. (rostlab.org)
Methods: The RNA-sequencing was performed to screen differential TFs in breast cancer subtypes. (bvsalud.org)
BACKGROUND: The continued development of targeted therapeutics for cancer treatment has required the concomitant development of more expansive methods for the molecular profiling of the patient's tumor. (jax.org)
CONCLUSIONS: There is a lack of consensus in the molecular diagnostics field on the best method for the validation of NGS-based assays in oncology, thus the importance of communicating methods, as contained in this report. (jax.org)
In this part of the wiki we present our results on different sequence based prediction methods. (tu-muenchen.de)
The study of microbial communities from environment- and human-derived samples through Next Generation Sequencing (NGS) methods has revealed a vast complexity in those ecological niches where hundreds or thousands of microbial species co-inhabit and functionally interact. (biomedcentral.com)
These methods take advantage of the different types of DNA nucleotide sequence variations demonstrated by the different species of parasites within a particular genus. (medscape.com)

In addition, annotations are classified as classical genetics or high-throughput (e.g., large scale survey, systematic mutation set). (yeastgenome.org)
Since then it is involved in different aspects of fungal molecular genetics. (marinefungi.eu)
Blueprint Genetics' Plus Analysis is a combination of both sequencing and deletion/duplication (copy number variant (CNV)) analysis. (blueprintgenetics.com)
Performance of Blueprint Genetics high-quality, clinical grade NGS sequencing assay for panels. (blueprintgenetics.com)

We developed a new approach to address this challenge, combining long-range PCR and nanopore sequencing with a novel bioinformatics pipeline. (nature.com)
I am an early career scientist interested in the evolution of deep eukaryote lineages and have therefore developed extensive skills in culturing, sequencing, phylogenetics and bioinformatics. (uio.no)
PathOS enables bioinformatics filtering, classification of variants, annotation, curation and clinical reporting all in a ISO15189 accredited framework. (petermac.org)
Raju K. Pillai, M.D., is an assistant clinical professor specializing in hematopathology, molecular pathology and pathology bioinformatics. (cityofhope.org)
Collection of open-source PHP code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other bioinformatics tools. (open-bio.org)
Molecular typing by multiple-locus variable number tandem repeat analysis (MLVA) was determined from closed genome assemblies using a custom bioinformatics pipeline (wgsMLVA). (cdc.gov)
EGE also develops epigenomic methodologies, profiling strategies, and bioinformatics tools, applicable to population-based cohorts and molecular epidemiology studies coordinated by IARC researchers and external collaborators. (who.int)

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)
Comparative analysis among different molluscan species clearly revealed that, while D. reticulatum neuropeptide sequences are conserved in Mollusca, there are also some unique features distinct from other members of this species. (oregonstate.edu)
The overall base composition is 31.0% A, 12.2% C, 17.7% G, and 39.1% T. Based on phylogenetic analysis using the amino acid sequences of PCGs, D. reticulatum was shown to be closely related to other species of Stylommatophora. (oregonstate.edu)
Nonetheless, the molecular basis of cellular responses to Pi-limitation and concurrent lipid accumulation by oleaginous species remains elusive. (biomedcentral.com)

Recently, the Molecular Atlas of Lung Development Program (LungMAP) was funded by the National Heart, Lung, and Blood Institute to develop an integrated open access database (known as BREATH) to characterize the molecular and cellular anatomy of the developing lung. (biomedcentral.com)

Despite the enrichment of these molecular quantitative trait loci (QTL) at evolutionarily volatile promoters, this does not translate into a corresponding enrichment of phenotypic traits mapping to these loci. (biomedcentral.com)
BioSamples SAMN31437443-SAMN31437454 contain raw sequencing reads from RNA-seq, whereas raw sequencing reads from target enrichment are available under SAMN31439307-SAMN31439402. (datadryad.org)

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)
The DNA sequence, annotation and analysis of human chromosome 3. (mpg.de)
Whole Genome Sequencing (WGS) is a tool providing quick and inexpensive approaches for analysis of food-borne pathogen epidemics. (elsevier.com)
Thus, genomic sequencing and phylogenomic analysis of isolates is essential to identify outbreaks and limit their occurrence and spread. (nationaljewish.org)
The ANTIMIC database has keyword search option and has integrated tools to aid the analysis at molecular level. (iscb.org)
The integrated tools include BLAST module for the analysis of similarity of query sequence to the ANTIMIC database content, and a peptide structure viewer module. (iscb.org)
The advent of next-generation sequencing (NGS) technologies for the comprehensive analysis of human antibody repertoires has opened up a new way of looking at B-cell immune landscapes with unprecedented resolution. (frontiersin.org)
Next Generation Sequencing analysis of diseased somatic cells, genome wide annotations of biomarkers, systems pathology studies, discovering of novel compounds are examples of the great advantages that high-performance computing can provide to omics science, providing a fast translation of biomolecular results to the clinical practice. (hindawi.com)
EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. (open-bio.org)
Sequence analysis: Multiple sequence alignment, sequence search and clustering, function prediction, motif discovery, functional site recognition in protein, RNA and DNA sequences. (wikicfp.com)
However, the impact of the complexity of gene annotations on DE analysis remains unclear. (elsevier.com)
Results: Using "mappability", a metric of the complexity of gene annotation, we compared three distinct human gene annotations, GENCODE, RefSeq, and NONCODE, and evaluated how mappability affected DE analysis. (elsevier.com)
Conclusions: We assessed how the complexity of gene annotations affects DE analysis using mappability. (elsevier.com)
Our findings indicate that the growth and complexity of gene annotations negatively impact the performance of DE analysis, suggesting that an approach that excludes unnecessary gene models from gene annotations improves the performance of DE analysis. (elsevier.com)
The laboratory also was involved in analysis and annotation of fungal genome sequences. (marinefungi.eu)
Plus analysis increases the likelihood of finding a genetic diagnosis for your patient, as large deletions and duplications cannot be detected using sequence analysis alone. (blueprintgenetics.com)

The development of PathOS is also targeted at institutions beyond Peter Mac that perform high throughput clinical sequencing. (petermac.org)
More recent advances in NGS technologies have led to the high-throughput sequencing of entire antibody variable heavy (VH) and light (VL) chains as well as natively paired VH:VL repertoires resulting in the identification of complete antibody clonotypes. (frontiersin.org)
We will use a newly developed, high throughput experimental strategy to identify these sequences that are engaged in gene activation in the mouse embryonic stem cells, embryonic fibroblasts, and a panel of embryonic and adult tissues. (encodeproject.org)
Different sets of gene annotations are available for the human genome and are continually updated-a process complicated with the development and application of high-throughput sequencing technologies. (elsevier.com)
SGD has manually curated and high-throughput GO Annotations, both derived from the literature, as well as computational, or predicted, annotations. (yeastgenome.org)
Two-Hybrid), annotation type (e.g., manual or high-throughput), and a reference, as well as other experimental details. (yeastgenome.org)

In recentyears, a number of diverse plant proteins with low sequence similarity toBet v 1 was identified. (embl.de)
A distance-based phylogenetic treeyielded a classification into 11 subfamilies, nine exclusively containingplant sequences and two subfamilies of bacterial proteins. (embl.de)
The superfamily of leucine-rich repeat proteins can be subdivided into at least six subfamilies, characterised by different lengths and consensus sequences of the repeats. (embl.de)
Here, we propose predicting GO terms through annotation transfer based on proximity of proteins in the SeqVec embedding rather than in sequence space. (rostlab.org)
Overall, this new concept is likely to change the annotation of proteins, in particular for proteins from smaller families or proteins with intrinsically disordered regions. (rostlab.org)
Small peptides, especially those derived from natural proteins as inhibitory peptide aptamers (iPAs), can produce highly effective and selective blockade of specific nociceptive molecular pathways to reduce pain with minimal off-target effects. (lww.com)
Click "Protein Details" for further information about the protein such as half-life, abundance, domains, domains shared with other proteins, protein sequence retrieval for various strains, physico-chemical properties, protein modification sites, and external identifiers for the protein. (yeastgenome.org)

Hundreds of whole genome sequences from worldwide isolates of Leptospira spp. (gob.ar)

Annotation based on most significant BLAST alignment for each cluster. (biomedcentral.com)
I first got it to make alignment and trees of my sequences and it works well for those purposes. (geneious.com)
Sequence Alignment Tools: One Parallel Pattern to Rule Them All? (hindawi.com)
Alleles for common molecular typing loci (ptxP, ptxA, ptxB, fimH, and prn ) were assigned by genome alignment to a curated set of wild-type and deficient alleles using high-stringency. (cdc.gov)
Multiple sequence alignment (MSA) was used to locate the conserved residues. (avensonline.org)
PDF 44 KB) Additional file 7: Alignment of sequences mapping with the same reference sequence with identical accession number in the Greengenes database, and resulting in different digital T-RFs. (mdm2signaling.com)

This algorithm predicts the functional, molecular and phenotypic consequences of protein missense variants using hidden Markov models. (sanger.ac.uk)

Our results reveal tap water contamination in direct contact with patients and the usefulness of WGS to investigate bacterial molecular epidemiology. (rug.nl)

As a reference to the human genome, the mouse genome sequence has proved extremely valuable in gene annotation. (encodeproject.org)
See how the University of Washington used HiFi sequencing to uncover a key finding about ALS and the human genome. (pacb.com)

in water from dental chair units (DCUs) of a hospital dental ward and to perform its molecular characterization by whole-genome sequencing (WGS). (rug.nl)
Genome sequence-based molecular characterization was performed using either completed assemblies or individual sequencing reads. (cdc.gov)

Four isolates (designated strains TC112, TC129, TC147, and TC273) cultured from bovine urine during that study have now been fully sequenced and are compared herein. (jgenomics.com)

We found that mappability was significantly different among the human gene annotations. (elsevier.com)

Genome -scale metabolic networks which have been automatically derived through sequence comparison techniques are necessarily incomplete. (rsc.org)

Results of this study will provide a molecular classification of HCC and allow us to identify targets for chemoprevention and treatment. (hopkinsmedicine.org)
ProtoNet 4.0: A hierarchical classification of one million protein sequences. (vldb.org)

The sequence was a 93,629-bp plasmid encoding a single antimicrobial drug resistance gene, bla CTX-M-14 . (cdc.gov)

mRNA sequencing revealed 66,476 unigenes, and the differentially expressed unigenes (DEGs) were associated with several key pathways, including phenylpropanoid biosynthesis, sugar metabolism, and quinolizidine alkaloid biosynthesis pathways. (biomedcentral.com)
Molecular paThwayS criTical for cancer developMenT and progreSSion, ThuS enhancing The evidence baSe direcTly relevanT To STudieS of cancer cauSaTion and prevenTion. (who.int)

2022 ) Molecular Ecology Resources. (datadryad.org)

Functional annotation by BLASTx revealed 39,987 unigenes with hits, which were further categorized into important functional groups based on sequence abundance. (oregonstate.edu)

As far as we know, no other current annotation tool provides [splicing prediction tools], he said. (genomeweb.com)
The SBASE domain sequence resource, release 12: prediction of protein domain-architecture using support vector machines. (vldb.org)
Energy-based RNA consensus secondary structure prediction in multiple sequence alignments. (bierinformatik.de)
The new method improves on the older version of FATHMM and now incorporates ENCODE annotation for its prediction. (sanger.ac.uk)
These cover the prediction of secondary structure, disordered regions, transmembrane helices, signal peptides and GO annotations. (tu-muenchen.de)

We describe the validation of the JAX Cancer Treatment Profile™ (JAX-CTP™), a next generation sequencing (NGS)-based molecular diagnostic assay that detects actionable mutations in solid tumors to inform the selection of targeted therapeutics for cancer treatment. (jax.org)
An interaction annotation is composed of the interaction type, name of the interactor, assay type (e.g. (yeastgenome.org)

CONCLUSIONS: In this study, we have been able to advance in the knowledge of the genetic overlap existing in autoimmunity, thus shedding light on common molecular mechanisms of disease and suggesting novel drug targets that could be explored for the treatment of the autoimmune diseases studied. (cam.ac.uk)
However, the molecular mechanisms governing the responses to drought stress in S. tonkinensis at the transcriptional and posttranscriptional levels are not well understood. (biomedcentral.com)
This is the first study to simultaneously profile the expression patterns of mRNAs and miRNAs on a genome-wide scale to elucidate the molecular mechanisms of the drought stress responses of S. tonkinensis . (biomedcentral.com)
However, the molecular mechanisms underlying the biosynthesis of quinolizidine alkaloids are not well understood. (biomedcentral.com)
Although the mouse is widely used to model human lung development, function, and disease, our understanding of the molecular mechanisms involved in alveolarization of the peripheral lung is incomplete. (biomedcentral.com)

These embeddings originate from deep learned language models (LMs) for protein sequences (SeqVec) transferring the knowledge gained from predicting the next amino acid in 33 million protein sequences. (rostlab.org)

It shows a striking sequence similarity with the yeast factor HAP2/3. (embl-heidelberg.de)
Phylogeneticrelationships within the Bet v 1 family, defined as the group of proteinswith significant sequence similarity to Bet v 1, were determined byaligning 264 Bet v 1-related sequences. (embl.de)

Dr. Pillai's research interests include molecular pathogenesis of lymphomas and leukemias and the application of panomics technologies in diagnostic pathology. (cityofhope.org)
The maximum work on the molecular pathogenesis of Shigella has been performed in S. flexneri serotypes 5 and 2a. (avensonline.org)

Provide centralized and standard procurement, processing, storage, annotation, and distribution of human biospecimens and coordinate specimen collection across the COH Clinical Network. (cityofhope.org)

This achievement is heavily attributed to having high-quality, high-molecular-weight genomic DNA where reads longer than 20 Kb provided 10x coverage of the genome. (pacb.com)

Cartagenia's offerings lack the breadth of annotation found in Alamut HT and the visualization capabilities of Alamut, Blavier pointed out. (genomeweb.com)
Click "Interaction Details" to view all interaction annotations and evidence for this locus, including an interaction visualization. (yeastgenome.org)

The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C . (yeastgenome.org)

Molecular marker based taxonomical annotation using Mitochondrial COI gene sequencing confirmed the identity of the specimen. (bioone.org)

Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. (yeastgenome.org)

STING Report: convenient web-based application for graphic and tabular presentations of protein sequence, structure and function descriptors from the STING database. (vldb.org)
Download DNA or protein sequence, view genomic context and coordinates. (yeastgenome.org)
The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. (weinberginternational.com)

S4: structure-based sequence alignments of SCOP superfamilies. (vldb.org)

Peptides with experimental annotations on their anticancer action on breast and lung cancer cells. (uci.edu)

However, individual transcript sequences of the same gene can differ through naturally occurring variations (e.g. polymorphisms), each with its own valid existence. (origene.com)

Whole-genome multi-locus sequence typing (wgMLST) results indicate that all strains belong to the same cluster with two to four allele differences. (rug.nl)

The Colorado Cystic Fibrosis RDP has sequenced hundreds of NTM isolates from CF patients across the United States . (nationaljewish.org)
First 341 CF NTM Isolates Sequenced, Shown by Adjusted State of Origin. (nationaljewish.org)
Here, we report and compare the complete genome sequence of four recent isolates of L . borgpetersenii serovar Hardjo designated strain TC112, TC147, TC129, and TC273. (jgenomics.com)
Despite the small number of isolates studied, they were genetically diverse, as shown by the sequence types, the N. gonorrhoeae multiantigen sequence typing types and the tree. (who.int)

Molecular genetic testing is useful in uncertain or questionable cases, as well as for prenatal diagnosis and for screening family members of an affected individual. (medscape.com)

The molecular sequence of this clone aligns with the gene accession number as a point of reference only. (origene.com)
Accession numbers for chromosome 1 and chromosome 2 for each of the four strains, as well as genome annotation features, are provided in Table 1 . (jgenomics.com)

The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from the UniProt Knowledgebase (including isoforms) and selected UniParc records. (weinberginternational.com)

Anatomy1

Organisms1

Diseases1

Chemicals and Drugs9

Analytical, Diagnostic and Therapeutic Techniques and Equipment20

Phenomena and Processes36

Disciplines and Occupations5

Anthropology, Education, Sociology and Social Phenomena1

Technology, Industry, Agriculture2

Information Science42

Health Care9

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

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

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

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

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

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

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

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

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Molecular Sequence Annotation

Software

User-Computer Interface

Phylogeny

Computational Biology

Databases, Genetic

Sequence Alignment

Database Management Systems

Molecular Sequence Data

Sequence Analysis, DNA

Internet

Algorithms

Documentation

Sequence Analysis, Protein

Databases, Protein

Evolution, Molecular

Genomics

Databases, Nucleic Acid

Information Storage and Retrieval

Bayes Theorem

Genome

Base Sequence

Expressed Sequence Tags

Models, Genetic

Computer Graphics

Databases, Factual

Proteins

Likelihood Functions

Markov Chains

Fossils

Sequence Analysis

RNA, Ribosomal, 18S

Biological Evolution

Amino Acid Sequence

Monte Carlo Method

Vocabulary, Controlled

DNA, Mitochondrial

Computer Simulation

Genetic Variation

DNA, Ribosomal

Gene Expression Profiling

Genome, Bacterial

Natural Language Processing

Data Mining

Terminology as Topic

Oligonucleotide Array Sequence Analysis

Genome, Plant

Genome, Human

Proteome

Cluster Analysis

Gene Ontology

Sequence Analysis, RNA

Chromosome Mapping

Programming Languages

Artificial Intelligence

Proteomics

High-Throughput Nucleotide Sequencing

Protein Interaction Mapping

Genome, Fungal

Transcriptome

Knowledge Bases

Search Engine

Pattern Recognition, Automated

Genome, Archaeal

Semantics

Open Reading Frames

Genes

Abstracting and Indexing as Topic

Software Design

PubMed

Gene Library

Contig Mapping

Enzymes

Metabolic Networks and Pathways

Pseudogenes

Multigene Family

Genome, Protozoan

Conserved Sequence

Automation

Reproducibility of Results