Abstract:
:We present a novel web-based resource, Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, the functional Dictionary of Homologous Superfamilies (DHS) and PDBsum. Currently Gene3D provides annotation for 36 complete genomes (two eukaryotes, six archaea, and 28 bacteria). On average, between 30% and 40% of the genes of a given genome can be structurally annotated. Matches to structural domains are found using the profile-based method (PSI-BLAST). and a novel protocol, DRange, is used to resolve conflicts in matches involving different homologous superfamilies.
journal_name
Genome Resjournal_title
Genome researchauthors
Buchan DW,Shepherd AJ,Lee D,Pearl FM,Rison SC,Thornton JM,Orengo CAdoi
10.1101/gr.213802subject
Has Abstractpub_date
2002-03-01 00:00:00pages
503-14issue
3eissn
1088-9051issn
1549-5469journal_volume
12pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract::We present GERMLINE, a robust algorithm for identifying segmental sharing indicative of recent common ancestry between pairs of individuals. Unlike methods with comparable objectives, GERMLINE scales linearly with the number of samples, enabling analysis of whole-genome data in large cohorts. Our approach is based on ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.081398.108
更新日期:2009-02-01 00:00:00
abstract::While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amp...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.213959.116
更新日期:2017-05-01 00:00:00
abstract::Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color, single array detection, applied to large-scale genotyping of up to 12,000 SNPs per reaction. While generating 38,429 SNP ass...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.3185605
更新日期:2005-02-01 00:00:00
abstract::We report the development of a simplified cap analysis of gene expression (CAGE) protocol adapted for single-molecule sequencers that avoids second strand synthesis, ligation, digestion, and PCR. HeliScopeCAGE directly sequences the 3' end of cap trapped first-strand cDNAs. As with previous versions of CAGE, we better...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.115469.110
更新日期:2011-07-01 00:00:00
abstract::The initial comparison of the human and chimpanzee genome sequences revealed 16 genomic regions with an unusually high density of rapidly evolving genes. One such region is the whey acidic protein (WAP) four-disulfide core domain locus (or WFDC locus), which contains 14 WFDC genes organized in two subloci on human chr...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6004607
更新日期:2007-03-01 00:00:00
abstract::Transcriptional networks have been shown to evolve very rapidly, prompting questions as to how such changes arise and are tolerated. Recent comparisons of transcriptional networks across species have implicated variations in the cis-acting DNA sequences near genes as the main cause of divergence. What is less clear is...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.111765.110
更新日期:2010-12-01 00:00:00
abstract::In vivo analyses of the occurrence, subcellular localization, and dynamics of protein-protein interactions (PPIs) are important issues in functional proteomic studies. The bimolecular fluorescence complementation (BiFC) assay has many advantages in that it provides a reliable way to detect PPIs in living cells with mi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.231860.117
更新日期:2019-01-01 00:00:00
abstract::We describe a new method, Tag-seq, which employs ultra high-throughput sequencing of 21 base pair cDNA tags for sensitive and cost-effective gene expression profiling. We compared Tag-seq data to LongSAGE data and observed improved representation of several classes of rare transcripts, including transcription factors,...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.094482.109
更新日期:2009-10-01 00:00:00
abstract::Many CpG islands have tissue-dependent and differentially methylated regions (T-DMRs) in normal cells and tissues. To elucidate how DNA methyltransferases (Dnmts) participate in methylation of the genomic components, we investigated the genome-wide DNA methylation pattern of the T-DMRs with Dnmt1-, Dnmt3a-, and/or Dnm...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.2431504
更新日期:2004-09-01 00:00:00
abstract::Infections by Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) are the predominant cause of bloody diarrhea and hemolytic uremic syndrome in the United States. In silico comparison of the two complete STEC O157 genomes (Sakai and EDL933) revealed a strikingly high level of sequence identity in orthologous pr...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.4759706
更新日期:2006-06-01 00:00:00
abstract::Aberrant DNA methylation (DNAm) was first linked to cancer over 25 yr ago. Since then, many studies have associated hypermethylation of tumor suppressor genes and hypomethylation of oncogenes to the tumorigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.109678.110
更新日期:2011-04-01 00:00:00
abstract::We compare several commonly used expression-based gene clustering algorithms using a figure of merit based on the mutual information between cluster membership and known gene attributes. By studying various publicly available expression data sets we conclude that enrichment of clusters for biological function is, in g...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.397002
更新日期:2002-10-01 00:00:00
abstract::Long and short interspersed elements (LINEs and SINEs) are retroelements that make up almost half of the human genome. L1 and Alu represent the most prolific human LINE and SINE families, respectively. Only a few Alu elements are able to retropose, and the factors determining their retroposition capacity are poorly un...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.384802
更新日期:2002-09-01 00:00:00
abstract::The accurate mapping of clones derived from genomic regions containing complex arrangements of repeated elements presents special problems for DNA sequencers. Recent advances in the automation of optical mapping have enabled us to map a set of 16 BAC clones derived from the DAZ locus of the human Y chromosome long arm...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.112100
更新日期:2000-09-01 00:00:00
abstract::Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but compose only a small minority of the total sRNA pool; siRNA locus annotation...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.256750.119
更新日期:2020-03-01 00:00:00
abstract::The Drosophila Enhancer of split complex [E(spl)-C] is a remarkable complex of genes many of which are effectors or modulators of Notch signaling. The complex contains different classes of genes including four bearded genes and seven basic helix-loop-helix (bHLH) genes. We examined the evolution of this unusual comple...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.104794.109
更新日期:2010-07-01 00:00:00
abstract::Histone modifications are now well-established mediators of transcriptional programs that distinguish cell states. However, the kinetics of histone modification and their role in mediating rapid, signal-responsive gene expression changes has been little studied on a genome-wide scale. Vascular endothelial growth facto...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.149674.112
更新日期:2013-06-01 00:00:00
abstract::Sequence-specific DNA-binding transcription factors have widespread biological significance in the regulation of gene expression. However, in lower prokaryotes and eukaryotic metazoans, it is usually difficult to find transcription regulatory factors that recognize specific target promoters. To address this, we have d...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.086595.108
更新日期:2009-07-01 00:00:00
abstract::Recent computational and experimental work suggests that functional modules underlie much of cellular physiology and are a useful unit of cellular organization from the perspective of systems biology. Because interactions among modules can give rise to higher-level properties that are essential to cellular function, a...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.3847105
更新日期:2005-09-01 00:00:00
abstract::Recent advances toward the characterization of Alzheimer's disease (AD) have permitted the identification of a dozen of genetic risk factors, although many more remain undiscovered. In parallel, works in the field of network biology have shown a strong link between protein connectivity and disease. In this manuscript,...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.114280.110
更新日期:2011-03-01 00:00:00
abstract::A large fraction of the genes from sequenced organisms are of unknown function. This limits biological insight, and for pathogenic microorganisms hampers the development of new approaches to battle infections. There is thus a great need for novel strategies that link genotypes to phenotypes for microorganisms. We desc...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.137430.112
更新日期:2012-12-01 00:00:00
abstract::We report the construction of a dense linkage map of the rat genome integrating 767 simple sequence length polymorphism markers, combined over three crosses with high rates of polymorphism. F2 populations from WKY x S (n = 159), BN x S (n = 91), and BN x GK (n = 139) were selected and genotyped for combinations of mic...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.7.5.434
更新日期:1997-05-01 00:00:00
abstract::Single-cell sequencing (SCS) is a powerful new tool for investigating evolution and diversity in cancer and understanding the role of rare cells in tumor progression. These methods have begun to unravel key questions in cancer biology that have been difficult to address with bulk tumor measurements. Over the past five...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.191098.115
更新日期:2015-10-01 00:00:00
abstract::Evolutionary constraints on gene regulatory elements are poorly understood: Little is known about how the strength of transcription factor binding correlates with DNA sequence conservation, and whether transcription factor binding sites can evolve rapidly while retaining their function. Here we use the model of the NF...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6490707
更新日期:2007-09-01 00:00:00
abstract::Alternative splicing (AS) creates multiple mRNA transcripts from a single gene. While AS is known to contribute to gene regulation and proteome diversity in animals, the study of its importance in plants is in its early stages. However, recently available plant genome and transcript sequence data sets are enabling a g...
journal_title:Genome research
pub_type: 杂志文章,评审
doi:10.1101/gr.053678.106
更新日期:2008-09-01 00:00:00
abstract::Genome-scale metabolic models promise important insights into cell function. However, the definition of pathways and functional network modules within these models, and in the biochemical literature in general, is often based on intuitive reasoning. Although mathematical methods have been proposed to identify modules,...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5662207
更新日期:2007-04-01 00:00:00
abstract::Translocations are known to affect the expression of genes at the breakpoints and, in the case of unbalanced translocations, alter the gene copy number. However, a comprehensive understanding of the functional impact of this class of variation is lacking. Here, we have studied the effect of balanced chromosomal rearra...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.103622.109
更新日期:2010-05-01 00:00:00
abstract::Microsatellites are abundant in vertebrate genomes, but their sequence representation and length distributions vary greatly within each family of repeats (e.g., tetranucleotides). Biophysical studies of 82 synthetic single-stranded oligonucleotides comprising all tetra- and trinucleotide repeats revealed an inverse co...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.078303.108
更新日期:2008-10-01 00:00:00
abstract::Fish-mammal genomic comparisons have proved powerful in identifying conserved noncoding elements likely to be cis-regulatory in nature, and the majority of those tested in vivo have been shown to act as tissue-specific enhancers associated with genes involved in transcriptional regulation of development. Although most...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.4143406
更新日期:2006-04-01 00:00:00
abstract::Transcription factors canonically bind nucleosome-free DNA, making the positioning of nucleosomes within regulatory regions crucial to the regulation of gene expression. Using the assay of transposase accessible chromatin (ATAC-seq), we observe a highly structured pattern of DNA fragment lengths and positions around n...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.192294.115
更新日期:2015-11-01 00:00:00