• Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism (be it an animal, a plant, a fungus, a bacterium, an archaean, a protist or a virus) and to annotate protein-coding genes and other important genome-encoded features. (wikipedia.org)
  • DNA annotation or genome annotation is the process of identifying attaching biological information to sequences , and particularly in identifying the locations of genes and determining what those genes do. (wikipedia.org)
  • It is often reported that the goal of sequencing a genome is to obtain information about the complete set of genes in that particular genome sequence. (wikipedia.org)
  • The proportion of a genome that encodes for genes may be very small (particularly in eukaryotes such as humans, where coding DNA may only account for a few percent of the entire sequence). (wikipedia.org)
  • Such projects may also include gene prediction to find out where the genes are in a genome, and what those genes do. (wikipedia.org)
  • There may also be related projects to sequence ESTs or mRNAs to help find out where the genes actually are. (wikipedia.org)
  • In teleostean fish, two nanos1 genes were generated, probably during the Teleost specific whole genome duplication (3R). (nature.com)
  • using a redundancy criterion to identify reproducible sequence differences between related genes within gene families. (biomedcentral.com)
  • Analysis of these sequences revealed single base substitutions and single base indels are the most frequently observed form of sequence variation between genes within families in the dataset. (biomedcentral.com)
  • Functional annotation of gene sequences indicate functional classifications are not randomly distributed among gene families containing few or many genes. (biomedcentral.com)
  • The more recent duplication event in particular would be expected to result in many paralogous pairs of genes differing by relatively few sequence differences, thus complicating gene identification using ESTs. (biomedcentral.com)
  • Albeit minimally, the different analyses performed in this project provide some light in the function of ovine uterus and can be applied to other indigenous species that have no or limited genome data availability to discover novel and unknown genes and proteins. (mjas.my)
  • In contrast, many genes underwent positive selection in this order and the majority of these sequences are clade-specific. (nature.com)
  • The blast clade genomes contain more secretome and avirulence effector genes, which likely play key roles in the interaction between Pyricularia species and their plant hosts. (nature.com)
  • Gene ontology (GO) enrichment analyses of protein coding genes, proximal to the region of conservation, in both organisms highlighted similar GO classes like regulation of transcription and central nervous system development. (sissa.it)
  • In summary, we show that interesting genomic regions in zebrafish could be marked based on their sequence homology to a mouse lncRNA, overlap with ESTs and proximity to genes involved in nervous system development.Conclusions: Conservation at the sequence level can identify a subset of putative lncRNA orthologs. (sissa.it)
  • Network analysis from a wealth of heterogeneous data sources is particular useful to unveil functional clues and pinpoint unsuspected relevant genes. (ub.edu)
  • This tool will aid researchers in human genetics and related fields to understand the molecular role of the reported RP (and the closely related disease, Leber congenital amaurosis) genes as well as provide a rationale to identify novel candidates. (ub.edu)
  • PFAM domains related to the Matrix Metalloproteinase proteins were mapped onto the set of homologous sequences for distinct families of Matrix Metalloproteinase genes. (ub.edu)
  • Finding protein-coding genes in eukaryotic genomic sequences with in-silico methods remains an important challenge in computational genomics, despite many years of intensive research work. (biomedcentral.com)
  • A cross-species comparison of genomic sequences can help in predicting genes in the given query sequence. (biomedcentral.com)
  • Differential gene expression analysis identified a number of root-specific CYP genes. (techscience.com)
  • Genetic improvement of this important crop depends on a complete and through understanding of the genes that make up the genome and how they have evolved. (usda.gov)
  • A first step to understanding the soybean genome is to identify all genes in the genome and then to infer functions for them in order to identify genes that may play a role in traits of agronomic importance. (usda.gov)
  • AceView: gene:him-8, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView. (nih.gov)
  • The genome sequence will allow scientists to locate and identify genes that can improve and strengthen crops and increase yield in order to help solve the Earth's looming food crisis by creating new strains of the cereal crops that make up 60% of humankind's diet. (bio5.org)
  • We add 'notes' to the genome sequence to tell us where genes are and what they are doing. (ed.ac.uk)
  • This helps to lay a foundation for researchers working in livestock genetics and genomics and animal breeders to use the genome of sheep and goats to answer important questions about which genes are involved in disease resistance or fertility for example. (ed.ac.uk)
  • Genetic and molecular analyses have led to the identification, cloning and characterization of a few genes that contribute to parasitic fitness in the pathogens. (sisef.it)
  • Quantitative PCR and high-throughput methods, such as expressed sequence tag analysis, have been used for measuring gene expression and identifying subsets of elm genes that are differentially expressed in the presence of O. novo-ulmi . (sisef.it)
  • These analyses have also helped identify genes that were differentially expressed in DED fungi grown under defined experimental conditions. (sisef.it)
  • The ongoing annotation of these genomes should spark a new wave of interest in the DED pathosystem, as it should lead to the formal identification of genes modulating parasitic fitness. (sisef.it)
  • Primary annotations based on sequence similarity are linked to networks of systematic annotation in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and can be queried and computationally utilized in downstream analyses. (umsystem.edu)
  • Bioinformatics is limited to sequence, structural, and functional analysis of genes and genomes and their corresponding products and is often considered computational molecular biology. (limswiki.org)
  • Unusual mitochondrial genomes and genes. (umontreal.ca)
  • A microarray analysis identified cell-wall-associated defense genes as loliolide-responsive tomato genes, and exogenous JA application did not induce the expression of these genes. (bvsalud.org)
  • The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. (philarchive.org)
  • The S. purpurea mt genome contains 52 genes: 31 protein-coding, 18 tRNAs, and three rRNAs. (springeropen.com)
  • Since the 1980s, molecular biology and bioinformatics have created the need for DNA annotation. (wikipedia.org)
  • Also, as scientists understand more about the role of this noncoding DNA (often referred to as junk DNA), it will become more important to have a complete genome sequence as a background to understanding the genetics and biology of any given organism. (wikipedia.org)
  • Such EST data form a valuable foundation for the understanding of the gene composition and genomic biology of yet-to-be fully sequenced genomes [ 3 ]. (biomedcentral.com)
  • The first 18 months into the SWEGENE project, the fourth main effort within SWEGENE, bioinformatics, has not produced a proposal on how to meet the needs of the current bio- logical problem domain, or how they should advance into the near, and long term, future research areas within computational biology. (lu.se)
  • ab a Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street (slot 516), Little Rock, AR 72205-7199, USA. (rsc.org)
  • Genome Biology 8 (5), p. (mpg.de)
  • This thematic series of companion papers constitutes the initial exploration of the genome biology of the waterflea (Daphnia) building on the first complete crustacean genome sequence. (biomedcentral.com)
  • This chapter discusses how to facilitate some aspects of molecular biology research from the viewpoint of a computational biologist or an information scientist interested in constructing biological information systems. (nationalacademies.org)
  • Electronic collaboration in molecular biology is facilitated currently by a variety of shared database systems. (nationalacademies.org)
  • Molecular biology is the analysis and description of biological organisms at a molecular level. (nationalacademies.org)
  • Molecular biology has traditionally been conducted on a small scale. (nationalacademies.org)
  • From both a theoretical and practical perspective, molecular biology has been one of the great success stories of modem science. (nationalacademies.org)
  • More than 60 percent of all National Institutes of Health grants-covering a wide range of problems in medicine and biology-propose use of the molecular methods of cloning, mapping, or sequencing to investigate problems. (nationalacademies.org)
  • More than 70 percent of all articles indexed by the National Library of Medicine contain molecular biology subject headings. (nationalacademies.org)
  • At this time, the field of molecular biology is diverging. (nationalacademies.org)
  • It is this side of molecular biology that is data intensive and is embodied in the Human Genome Project, a burgeoning scientific endeavor producing vast amounts of new information that researchers must select from to advance their investigations. (nationalacademies.org)
  • My undergraduate degree was in Animal Biology and for my PhD I used molecular phylogenetics to characterise the bacterial symbionts of insects. (ed.ac.uk)
  • Computers became essential in molecular biology when protein sequences became available after Frederick Sanger determined the sequence of insulin in the early 1950s. (ind.in)
  • The items in this collection are the scholarly output of the faculty, staff, and students of the Division of Molecular Biology and Biochemistry. (umsystem.edu)
  • However, rapid developments in genomic, molecular research, and information technologies have combined to produce a tremendous amount of information related to molecular and other types of biology. (limswiki.org)
  • The development of these computational tools depended on knowledge generated from a wide range of disciplines including mathematics, statistics, computer science, information technology, and molecular biology. (limswiki.org)
  • In: RNA Metabolism in Mitochondria, book series "Nucleic Acids and Molecular Biology" (eds J.Cruz-Reyes, MW. (umontreal.ca)
  • In: Expressed sequence tags - generation and analysis, Methods in Molecular Biology Vol. 533 (J. Parkinson, ed. (umontreal.ca)
  • We are also interested in evolutionary computational biology on sequence, cellular, and organismal level. (univ-amu.fr)
  • We currently have several projects related to evolutionary computational biology. (univ-amu.fr)
  • The Web site "www.artichokegenome.unito.it" hosts all the available genomic sequences, together with their structural/functional annotations and project information are presented to users via the open-source tool JBrowse, allowing the analysis of collinearity and the discovery of genomic variants, thus representing a one-stop resource for Cynara cardunculus genomics. (researchgate.net)
  • Genomics Lab C omp G en L ab C.G.L. (ub.edu)
  • His recent research interests include genome editing to engineer immunity against viral infection and using the next generation sequencing to explore viral population genomics and genetic diversity and to discover new viruses and novel viral strains. (bio5.org)
  • Rod Wing, PhD, and his lab, The Arizona Genomics Institute, specialize in building what geneticists call a physical map of a genome- a crucial foundation of any genome sequencing effort. (bio5.org)
  • [3] [4] Its primary use since at least the late 1980s has been in genomics and genetics, particularly in those areas of genomics involving large-scale DNA sequencing . (limswiki.org)
  • The Human Genome Project is a well known example of a genome project. (wikipedia.org)
  • However, large-scale nucleotide sequencing directed at the human genome (3 billion nucleotides! (nationalacademies.org)
  • When I first started doing research, our knowledge on livestock genomes was not even close to our knowledge on the human genome, so that really inspired me to work in this field. (ed.ac.uk)
  • Assembly of the human genome is one of the greatest achievements of bioinformatics. (ind.in)
  • Toward this objective, ChIP-Seq data of 14 S/MAR binding proteins were analyzed and the binding site coordinates of these proteins were used to prepare a non-redundant S/MAR dataset of human genome. (researchgate.net)
  • and the formal start of the Human Genome Project in 1990. (limswiki.org)
  • Genome assembly refers to the process of taking a large number of short DNA sequences and reassembling them to create a representation of the original chromosomes from which the DNA originated. (wikipedia.org)
  • A genome assembly algorithm works by taking all the pieces and aligning them to one another, and detecting all places where two of the short sequences, or reads, overlap. (wikipedia.org)
  • Genome assembly is a very difficult computational problem, made more difficult because many genomes contain large numbers of identical sequences, known as repeats. (wikipedia.org)
  • An example of such assembler Short Oligonucleotide Analysis Package developed by BGI for de novo assembly of human-sized genomes, alignment, SNP detection, resequencing, indel finding, and structural variation analysis. (wikipedia.org)
  • The first high-quality genome assembly of the globe artichoke has been produced within the Compositae Genome Project and the resequencing analyses of four globe artichoke genotypes, representative of the core varietal types, as well as a genotype of the related taxa cultivated cardoon was, later on, carried out. (researchgate.net)
  • 1 ]) may delay a full sequence assembly. (biomedcentral.com)
  • Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, genome-wide association studies, and the modeling of evolution. (limswiki.org)
  • [click here to continue…] 2015) Next-Generation Sequencing and Assembly of Plant Genomes. (steirer-fans.de)
  • Dr. Deanna Church , NCBI project lead for the Genome Reference Consortium (GRC) and projects such as Map Viewer, Ideogram Service, Coordinate Remapping Service and CloneDB, spoke about The Human Reference Assembly and Resources for Navigating Genomic Information. (nih.gov)
  • In: Organelle Genetics 2012, Part 2: evolution of organelle genomes and gene expression (C. Bullerwell, ed), Springer-Verlag Heidelberg, Germany, p. 41-77. (umontreal.ca)
  • Our analysis contributes toward understanding the organization and evolution of organelle genomes in Salicaceae species. (springeropen.com)
  • See also our pages on BioInformatics and on the Trypanosoma cruzi Genome Initiative. (fiocruz.br)
  • A secondary goal that should be sought by a bioinformatics facility is to make algorithms and analysis methods accessible for non-computational biologists. (lu.se)
  • Another early contributor to bioinformatics was Elvin A. Kabat , who pioneered biological sequence analysis in 1970 with his comprehensive volumes of antibody sequences released with Tai Te Wu between 1980 and 1991. (ind.in)
  • As whole genome sequences became available, again with the pioneering work of Frederick Sanger, the term bioinformatics was re-discovered to refer to the creation of databases such as GenBank in 1982. (ind.in)
  • With the public availability of data tools for their analysis were quickly developed and described in journals such as Nucleic Acids Research which published specialized issues on bioinformatics tools as early as 1982. (ind.in)
  • Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data. (ind.in)
  • Results We describe a bioinformatics pipeline known as FunnyBase that has been used to store, annotate, and analyze 40,363 expressed sequence tags (ESTs) from the heart and liver of the fish, Fundulus heteroclitus. (umsystem.edu)
  • DNA microarray technology aids in gene expression analysis and other bioinformatics functions. (limswiki.org)
  • Bioinformatics now entails the creation and advancement of databases, algorithms, computational, and statistical techniques and theory to solve formal and practical problems arising from the management and analysis of biological data. (limswiki.org)
  • Common activities in bioinformatics include mapping and analyzing DNA and protein sequences, aligning different DNA and protein sequences to compare them, and creating and viewing 3-D models of protein structures. (limswiki.org)
  • Arguably one of the first "bioinformatics" projects-though the concept didn't yet exist-involved the 1965 creation and maintenance of a protein sequence database called the Atlas of Protein Sequence and Structure by Margaret O. Dayhoff, Richard V. Eck, and Robert S. Ledley. (limswiki.org)
  • Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data, including nucleotide and amino acid sequences, protein domains, and protein structures. (limswiki.org)
  • Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date. (biomedcentral.com)
  • Here we report the construction of 12 BAC/BES framework physical maps derived from these libraries and an analysis of the BESs in terms of transposable element, simple sequence repeat (SSR), microRNA (miRNA), and single nucleotide variation (SNV) content. (biomedcentral.com)
  • extended the number of clusters in the ECC to 18 phylogenomic groups (A-R) by analyzing core single-nucleotide polymorphisms (SNPs) in 390 whole genomes ( 15 ). (cdc.gov)
  • New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. (mpg.de)
  • Our research in plant and animal genomes, at the whole genome and transcriptome levels, will impact successful genetic selections toward the goal of feeding the 9 billion people toward the year 2050. (bio5.org)
  • The SSR markers were validated via an in silico based PCR analysis adopting two available assembled transcriptomes, derived from contrasting globe artichoke accessions, as templates. (researchgate.net)
  • To this end, we recently sequenced the genomes of five species and generated transcriptomes from 21 species of Magnaporthales, including saprobes and plant pathogens 9 . (nature.com)
  • We believe this study will result useful as a reference to analyze the conservation of lncRNAs in newly sequenced genomes and transcriptomes. (sissa.it)
  • From human MMP sequences, four S.mediterranea homologs were found on planarian transcriptomes. (ub.edu)
  • Taking advantage of digital gene expression (DGE) sequencing technology we compare all the available transcriptomes for S. mediterranea and improve their annotation. (ub.edu)
  • with analyses of structural variation, gene modeling and transcriptomes. (bio5.org)
  • The layered design of the database can handle the multiplicity of transcriptome-specific networks, facilitates the comparison among them, and allows the integration of newly sequenced/assembled transcriptome versions. (ub.edu)
  • This study conducted a comparative analysis of the T. wilfordii transcriptome derived from its root and leaf tissues. (techscience.com)
  • A combination of large-scale in-house sequencing, gene expression profiling and public sequence and gene expression data mining were used to characterise the transcriptome of NSCLC and the data used to generate a disease-focused microarray - the Lung Cancer DSA research tool. (biomedcentral.com)
  • The mammalian transcriptome has been estimated to consist of as many as 10 7 RNAs [ 23 ] and it has been suggested that the transcript rather than the gene should be regarded as the operational unit of the genome [ 24 ]. (biomedcentral.com)
  • Historically, when sequencing eukaryotic genomes (such as the worm Caenorhabditis elegans) it was common to first map the genome to provide a series of landmarks across the genome. (wikipedia.org)
  • Long terminal repeat (LTR) retroelements represent a successful group of transposable elements (TEs) that have played an important role in shaping the structure of many eukaryotic genomes. (biomedcentral.com)
  • The first group consists of ab initio programs which use only the query genomic sequence as input. (biomedcentral.com)
  • The second group of gene-finding methods, extrinsic methods, comprises all programs which use data other than the query genomic sequence. (biomedcentral.com)
  • We assembled the complete Salix purpurea L. mt genome by screening genomic sequence reads generated by a Roche-454 pyrosequencing platform. (springeropen.com)
  • HMMGene, has an extension that integrates into the HMM information from BLAST alignments of the query sequence with cDNA, EST and protein sequences [ 15 ]. (biomedcentral.com)
  • This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones. (nih.gov)
  • Click on any transcript to open the specific mRNA page, to see the exact cDNA clone support and eventual SNPs and to get details on tissues, sequences, mRNA and protein annotations. (nih.gov)
  • Proteins supported by a single continuous cDNA sequence lead to underlining the name/ending of the variant. (nih.gov)
  • A pink broken line denotes an intron with standard boundaries (gt-ag or gc-ag) that is exactly supported (i.e. a cDNA sequence exactly matches the genome over 16 bp, 8 on both sides of the intron). (nih.gov)
  • An integrated framework for cDNA library production, sequencing, quality control, expression data generation, and systems-level analysis is presented and utilized. (umsystem.edu)
  • The current challenge in human molecular genetics is to bridge the gap between genotype and phenotype, particularly in highly heterogeneous monogenic disorders, such as retinitis pigmentosa (RP), as well as in polygenic and complex diseases. (ub.edu)
  • The genetics of tropical adaptation, advances in genome sequencing, colourful lambs and her love of animals. (ed.ac.uk)
  • Recently, I started a Fellowship that integrates the sheep and goat gene expression atlas projects with research on small ruminants from African countries, including Ethiopia and Cameroon, working within the Centre for Tropical Livestock Genetics and Health. (ed.ac.uk)
  • Unexpectedly complex mitoribosomes in Andalucia godoyi , a protist with the most bacteria-like mitochondrial genome. (umontreal.ca)
  • Gene fragmentation and RNA editing without borders: eccentric mitochondrial genomes of diplonemids. (umontreal.ca)
  • Mitochondrial genomes of algae. (umontreal.ca)
  • Mitochondrial Genome Evolution. (umontreal.ca)
  • Mitochondrial genome organization and evolution within the green algae and land plants. (umontreal.ca)
  • Plant mitochondrial (mt) genomes possess several complex features, including a variable size, a dynamic genome structure, and complicated patterns of gene loss and gain throughout evolutionary history. (springeropen.com)
  • The mitochondrial (mt) genome has drawn increased attention during the genomic and now post-genomic eras owing to its maternal pattern of inheritance and unique evolutionary features, and is often used for the phylogenetic study of plants (Gualberto et al. (springeropen.com)
  • With the development of next generation sequencing (NGS) technologies, such as the Roche and Illumina platforms, new strategies are being used to characterize plant mitochondrial genomes. (springeropen.com)
  • A computational evaluation of the lncRNAs through systematic conservation analyses of both sequences as well as their genomic architecture is required.Results: Our results show that a subset of mouse candidate lncRNAs could be distinguished from random sequences based on their alignment with zebrafish phastCons elements. (sissa.it)
  • Phylogenetic reconstruction over the protein sequence alignment was computed by RAxML . (ub.edu)
  • Dayhoff compiled one of the first protein sequence databases, initially published as books and pioneered methods of sequence alignment and molecular evolution. (ind.in)
  • The identification of potential gene sequences (pHaps) from soybean allows us to begin to get a picture of the genomic history of the organism as well as begin to observe the evolutionary fates of gene copies in this highly duplicated genome. (biomedcentral.com)
  • We identified approximately 45,000 potential gene sequences (pHaps) from EST sequences of Williams/Williams82, an inbred genotype of soybean ( Glycine max L. Merr. (biomedcentral.com)
  • This study examined potential gene sequences identified in EST libraries of soybean and assigned the potential gene sequences with molecular functions. (usda.gov)
  • In this study, we generated genome sequence data from five additional Magnaporthales fungi including non-pathogenic species, and performed comparative genome analysis of a total of 13 fungal species in the class Sordariomycetes to understand the evolutionary history of the Magnaporthales and of fungal pathogenesis. (nature.com)
  • The paucity of studies and the lack of sequence data from non-model species in Magnaporthales results in a poor understanding of the phylogeny and an unstable taxonomy of Magnaporthales species. (nature.com)
  • Furthermore, genome data from non-pathogen lineages are necessary to provide a more robust comparative genomic framework to help place the rice blast fungus in an evolutionary context and to understand the evolution of pathogenesis and other characters of these important organisms. (nature.com)
  • We hereby present the methodology used to gather information from several publicly available datasets, generate a computational analysis framework on a core network data structure, and provide a user-friendly web interface ( RPGeNet ) to explore that network. (ub.edu)
  • Some of the best available ab initio gene prediction programs have been extended and have become more accurate by exploiting additional extrinsic data sources such as protein or EST sequences [ 13 ]. (biomedcentral.com)
  • Data integration using scanners with SQL output--the bioscanners project at sourceforge. (mpg.de)
  • GOblet: annotation of anonymous sequence data with Gene Ontology and pathway terms. (mpg.de)
  • In addition several prototypes that support collaboration are in use now, and a model collaboratory, the Worm Community System, illustrates a potential future direction for community information systems that support retrieval, analysis, and sharing of essential data and literature. (nationalacademies.org)
  • EU COST Next generation sequencing data analysis network and training consortium. (mpg.de)
  • Resources such as mass-produced microarrays and the computational tools linking these data to functional annotation at the system and pathway level are rarely available for non-model species. (umsystem.edu)
  • Therefore, these data will help toward better understanding of genome functioning and designing effective anti-viral therapeutics. (researchgate.net)
  • A flurry of genome studies went on to produce unprecedented amounts of biological data, creating a sudden demand for rapid and efficient computational tools to manage and analyze the data. (limswiki.org)
  • Herein, we detail the development and application of a hierarchical machine learning model to rapidly identify and trace the geographical source of S. Enteritidis infections from whole genome sequencing data. (elifesciences.org)
  • This important study presents a machine learning-based classifier that can accurately determine the geographic origin of a Salmonella enterica sample from its whole-genome sequencing data in under five minutes leading to actionable public health insights. (elifesciences.org)
  • Applying the method to 2,313 whole genome sequences collected in the United Kingdom and several external validation datasets, the authors provide convincing evidence that Salmonella genomic data can be used to identify the likely geographic source of a food-borne outbreak and, in most cases, correctly identify the country of origin of an infection acquired overseas. (elifesciences.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)
  • Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. (philarchive.org)
  • As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (philarchive.org)
  • The edges are scored according to information on enzymes from the EST data. (biomedcentral.com)
  • Our lab is developing user-friendly tools for general data analysis, data mining and data integration for the research community. (univ-amu.fr)
  • We generated the mt genome sequence from 454 pyrosequencing whole genome big data. (springeropen.com)
  • Large scale gene analysis of most organisms is hampered by incomplete genomic sequences. (biomedcentral.com)
  • In many organisms, such as soybean, the best source of sequence information is the existence of expressed sequence tag (EST) libraries. (biomedcentral.com)
  • Molecular biologists have made many important theoretical advances from such comparisons, notably elucidation of the central role of DNA (deoxyribonucleic acid) as the carrier of genetic information in all free-living organisms. (nationalacademies.org)
  • Several attempts have been made toward identification of S/MARs in genomes of various organisms including human. (researchgate.net)
  • Based on phylogenetic and synteny analyses, this study reveals that nanos1 gene has undergone multiple duplications and gene copies losses in Vertebrates. (nature.com)
  • Further phylogenetic analysis suggested specific family members of CYPs that may participate in the late steps during celastrol biosynthesis. (techscience.com)
  • 1997 ). The comparative analysis of plant mt genomes enhances our understanding of genome rearrangement and DNA transfer mechanisms, and of phylogenetic diversity. (springeropen.com)
  • Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention. (mpg.de)
  • Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement. (mpg.de)
  • Originally, most large-scale DNA sequencing centers developed their own software for assembling the sequences that they produced. (wikipedia.org)
  • However, this has changed as the software has grown more complex and as the number of sequencing centers has increased. (wikipedia.org)
  • With the advancement of next-generation sequencing and mass spectrometry, there is a growing need for the ability to merge biological features in order to study a system as a whole. (rsc.org)
  • Of these, three miRNAs were differentially expressed miRNAs and 18 miRNAs involved in sexual differentiation as determined by functional analysis with GO annotation and KEGG pathway analysis. (peerj.com)
  • Many EST libraries were constructed from RNA extracted from various genetic backgrounds, thus gene identification from these sources is complicated by the existence of both gene and allele sequence differences. (biomedcentral.com)
  • In the current study, we sequenced two small non-coding RNA libraries made from the gonads of adult male and female budgerigars using Illumina paired-end sequencing technology. (peerj.com)
  • During this process and the subsequent rehydration, metabolites were measured in a time series by GC-MS. Additionally expressed sequence tags are available, especially libraries generated from the active and inactive state. (biomedcentral.com)
  • 2015 ), have been successfully assembled through a combination approach using shotgun and paired-end NGS sequencing from non-enriched whole genome DNA libraries. (springeropen.com)
  • The idea was also to propose a framework where the SWEGENE platform users would get computerised support for their research projects. (lu.se)
  • We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the 10 genome types of Oryza aligned to the O. sativa ssp. (biomedcentral.com)
  • The M. phaseolina genome provides a framework of the infection process at the cytological and molecular level which uses a diverse arsenal of enzymatic and toxin tools to destroy the host plants. (biomedcentral.com)
  • They can bind to the 3′ untranslated region (3′UTR) of target messenger RNAs (mRNAs) in order to regulate gene expression post-transcriptionally with no sequence specificity but by potential electrostatic interactions with the phosphate backbone of RNA 2 , 3 . (nature.com)
  • Finally, analysis of transposable elements (TE) showed differing proportions of TE classes among Magnaporthales genomes, suggesting that species-specific patterns may hold clues to the history of host/environmental adaptation in these fungi. (nature.com)
  • Until recently, however, functional analysis of the DED fungi was hampered by the lack of protocols for efficient gene knockout and by the unavailability of a full genome sequence. (sisef.it)
  • The small genomes of the DED fungi also facilitate genomic analyses. (sisef.it)
  • Differentially expressed miRNAs target 49 transcripts and their gene ontology enrichment analysis showed that the susceptible cultivar responds by modulating the processes of protein localization and pigment synthesis, whereas the resistant cultivar responds by modulating transcription factors and hormone signalling. (researchsquare.com)
  • The two successive nanos gene duplications may result from the second and third whole genome duplication events at the basis of Vertebrates and Teleosts respectively. (nature.com)
  • Timing and mechanism of ancient vertebrate genome duplications - the adventure of a hypothesis. (mpg.de)
  • The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism. (wikipedia.org)
  • For a bacterium containing a single chromosome, a genome project will aim to map the sequence of that chromosome. (wikipedia.org)
  • For the human species, whose genome includes 22 pairs of autosomes and 2 sex chromosomes, a complete genome sequence will involve 46 separate chromosome sequences. (wikipedia.org)
  • Rather than sequence a chromosome in one go, it would be sequenced piece by piece (with the prior knowledge of approximately where that piece is located on the larger chromosome). (wikipedia.org)
  • With hints from EST and protein databases, our new approach was able to predict 89% of the exons in human chromosome 22 correctly. (biomedcentral.com)
  • Our strategy is to develop bacterial artificial chromosome (BAC)-end sequence (BES) physical frameworks of the ten genome types of Oryza and align them to the reference sequence. (biomedcentral.com)
  • When I first joined The Roslin Institute, I led the sheep gene expression atlas project, which was a large project that looked at gene expression in all tissues and cell types in sheep. (ed.ac.uk)
  • Western blotting of testis tissues revealed two bands, at positions corresponding to a molecular weight of approximately 26 kDa. (bvsalud.org)
  • The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. (philarchive.org)
  • Upon functional annotation to both unigenes and CDS, binding and catalytic activity were the two most common molecular function while the most common biological processes were related to cellular processes. (mjas.my)
  • This type of "systems-level" analysis is critical to the understanding of patterns of gene expression that underlie biological processes. (umsystem.edu)
  • In a second project, we use complex networks to investigate the temporal behaviour of biological systems - monitored by temporal protein or RNA expression dynamics. (univ-amu.fr)
  • Feb 22: Deanna Church, NCBI project lead for the Genome Reference Consortium (GRC), will speak about Map Viewer, Ideogram Service, Coordinate Remapping Service and CloneDB. (nih.gov)
  • Some extrinsic methods use genomic sequences from other species. (biomedcentral.com)
  • Other extrinsic methods use a database of known expressed sequences or proteins. (biomedcentral.com)
  • For example, there are methods to locate a gene within a sequence, to predict protein structure and/or function, and to cluster protein sequences into families of related sequences. (ind.in)
  • Pfam protein family related to electron transport process towards the production of ATP family, was additionally identified among the ESTs. (mjas.my)
  • Analysis of ESTs with Pfam revealed the importance of ATP generation in the uterus. (mjas.my)
  • In 2013, the genome sequences of O. ulmi and O. novo-ulmi were publicly released. (sisef.it)
  • Longitudinal analysis and validation with publicly accessible international samples indicated that predictions were robust to prospective external datasets. (elifesciences.org)
  • More than 177,000 perfect SSRs were revealed, equivalent to an overall density across the genome of 244.5 SSRs/Mbp, but some 224,000 imperfect SSRs were also identified. (researchgate.net)
  • Simple sequence repeats (SSRs) are highly variable features of all genomes. (biomedcentral.com)
  • Genomic sequencing of selected loci indicate that intron-like intervening sequences are numerous and are approximately 220 bp in length. (biomedcentral.com)
  • In a shotgun sequencing project, all the DNA from a source (usually a single organism, anything from a bacterium to a mammal) is first fractured into millions of small pieces. (wikipedia.org)
  • In many ways genome projects do not confine themselves to only determining a DNA sequence of an organism. (wikipedia.org)
  • The complete amount of DNA that defines any living organism is known as its genome. (nationalacademies.org)
  • Changes in technology and in particular improvements to the processing power of computers, means that genomes can now be 'shotgun sequenced' in one go (there are caveats to this approach though when compared to the traditional approach). (wikipedia.org)
  • These isolates formed a new subgroup in the E . hormaechei metacluster, according to their hsp60 sequences and phylogenomic analysis. (cdc.gov)
  • An extensive literature documenting physiological and ecological diversity make Daphnia an ideal model to study the genetic architecture of phenotypic variation in natural populations and the evolution of genome structure/function relationships in aquatic environments. (biomedcentral.com)
  • PlanNET is a web application that stores predicted Schmidtea mediterranea protein-protein interactions (ppi) projected over a Human ppi network, in order to provide a transcript-centric exploration of the planarian interactome. (ub.edu)