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PubMed1999

The Genome Sequence DataBase: towards an integrated functional genomics resource.

During 1998 the primary focus of the Genome Sequence DataBase (GSDB; http://www.ncgr.org/gsdb ) located at the National Center for Genome Resources (NCGR) has been to improve data quality, improve data collections, and provide new methods and tools to access and analyze data. Data quality has been improved by extensive curation of certain data fields necessary for maintaining data collections and for using certain tools. Data quality has also been increased by improvements to the suite of programs that import data from the International Nucleotide Sequence Database Collaboration (IC). The Sequence Tag Alignment and Consensus Knowledgebase (STACK), a database of human expressed gene sequences developed by the South African National Bioinformatics Institute (SANBI), became available within the last year, allowing public access to this valuable resource of expressed sequences. Data access was improved by the addition of the Sequence Viewer, a platform-independent graphical viewer for GSDB sequence data. This tool has also been integrated with other searching and data retrieval tools. A BLAST homology search service was also made available, allowing researchers to search all of the data, including the unique data, that are available from GSDB. These improvements are designed to make GSDB more accessible to users, extend the rich searching capability already present in GSDB, and to facilitate the transition to an integrated system containing many different types of biological data.

Animals↗
PubMed2004

The genomic threading database.

UNLABELLED: The Genomic Threading Database currently contains structural annotations for the genomes of over 100 recently sequenced organisms. Annotations are carried out by using our modified GenTHREADER software and through implementing grid technology. AVAILABILITY: http://bioinf.cs.ucl.ac.uk/GTD

Database Management Systems↗
PubMed1996

Characterization and fine localization of two new genes in Xq28 using the genomic sequence/EST database screening approach.

Two new genes were identified and mapped by searching the EST databases with genomic sequences obtained from putative CpG islands of the rodent-human hybrid X3000. Previous mapping of these CpG islands in the proximity of the host cell factor (HCFC1) and GdX genes automatically localized these two new genes to Xq28 in the interval between the L1 cell adhesion molecule (L1CAM) and the glucose-6-phosphate dehydrogenase (G6PD) loci. Both genes are relatively short, contain an ORF of 261 and 105 amino acids, respectively, and are ubiquitously expressed. Combining sequencing of selected CpG islands, derived from hybrids containing small portions of the human genome, with an EST database search is an easy method of identifying and mapping new genes to specific regions of the genome.

Amino Acid Sequence↗
PubMed1996

The Genome Sequence DataBase (GSDB): meeting the challenge of genomic sequencing.

The genome sequence database (GSDB) is a complete, publicly available relational database of DNA sequences and annotation maintained by the National Center for Genome Resources (NCGR) under a Cooperative Agreement with the US Department of Energy (DOE). GSDB provides direct, client- server access to the database for data contributions, community annotation and SQL queries. The GSDB Annotator, a multi-platform graphic user interface, is freely available. Automatically updated relational replicates of GSDB are also freely available.

Amino Acid Sequence↗
PubMed1998

Databases in genomic research.

Genome-related databases have already become an invaluable part of the scientific landscape. The role played by these databases will only increase as the volume and complexity of relevant biology data rapidly expand. We are far enough into the genome project and into the development of these databases to assess their attributes and to reexamine some of the conceptual organizations and approaches they are taking. It is clear that there are needs for both highly detailed and simplified database views, the latter being especially needed to make expert domain data more accessible to nonspecialists.

Animals↗
PubMed2007

DroSpeGe: rapid access database for new Drosophila species genomes.

The Drosophila species comparative genome database DroSpeGe (http://insects.eugenes.org/DroSpeGe/) provides genome researchers with rapid, usable access to 12 new and old Drosophila genomes, since its inception in 2004. Scientists can use, with minimal computing expertise, the wealth of new genome information for developing new insights into insect evolution. New genome assemblies provided by several sequencing centers have been annotated with known model organism gene homologies and gene predictions to provided basic comparative data. TeraGrid supplies the shared cyberinfrastructure for the primary computations. This genome database includes homologies to Drosophila melanogaster and eight other eukaryote model genomes, and gene predictions from several groups. BLAST searches of the newest assemblies are integrated with genome maps. GBrowse maps provide detailed views of cross-species aligned genomes. BioMart provides for data mining of annotations and sequences. Common chromosome maps identify major synteny among species. Potential gain and loss of genes is suggested by Gene Ontology groupings for genes of the new species. Summaries of essential genome statistics include sizes, genes found and predicted, homology among genomes, phylogenetic trees of species and comparisons of several gene predictions for sensitivity and specificity in finding new and known genes.

Animals↗
PubMed2004

i-Genome: a database to summarize oligonucleotide data in genomes.

BACKGROUND: Information on the occurrence of sequence features in genomes is crucial to comparative genomics, evolutionary analysis, the analyses of regulatory sequences and the quantitative evaluation of sequences. Computing the frequencies and the occurrences of a pattern in complete genomes is time-consuming. RESULTS: The proposed database provides information about sequence features generated by exhaustively computing the sequences of the complete genome. The repetitive elements in the eukaryotic genomes, such as LINEs, SINEs, Alu and LTR, are obtained from Repbase. The database supports various complete genomes including human, yeast, worm, and 128 microbial genomes. CONCLUSIONS: This investigation presents and implements an efficiently computational approach to accumulate the occurrences of the oligonucleotides or patterns in complete genomes. A database is established to maintain the information of the sequence features, including the distributions of oligonucleotide, the gene distribution, the distribution of repetitive elements in genomes and the occurrences of the oligonucleotides. The database can provide more effective and efficient way to access the repetitive features in genomes.

Alu Elements↗
PubMed2004

3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes.

The 3D-GENOMICS database (http://www.sbg.bio. ic.ac.uk/3dgenomics/) provides structural annotations for proteins from sequenced genomes. In August 2003 the database included data for 93 proteomes. The annotations stored in the database include homologous sequences from various sequence databases, domains from SCOP and Pfam, patterns from Prosite and other predicted sequence features such as transmembrane regions and coiled coils. In addition to annotations at the sequence level, several precomputed cross- proteome comparative analyses are available based on SCOP domain superfamily composition. Annotations are available to the user via a web interface to the database. Multiple points of entry are available so that a user is able to: (i) directly access annotations for a single protein sequence via keywords or accession codes, (ii) examine a sequence of interest chosen from a summary of annotations for a particular proteome, or (iii) access precomputed frequency-based cross-proteome comparative analyses.

Amino Acid Sequence↗
PubMed2026

The Saccharomyces Genome Database-a history of ideas and accomplishments, 1994-2026.

The Saccharomyces Genome Database (SGD) is one of the longest-running and most consequential biological databases in the world. Founded in the early 1990s at Stanford University under the visionary leadership of David Botstein and developed under the long-term technical direction of J. Michael Cherry, SGD has served for more than three decades not only as the authoritative knowledge center for the budding yeast Saccharomyces cerevisiae, but also as the source for much of the fundamentals of eukaryotic biology. This history traces the arc of a remarkable intellectual and scientific project: beginning with the challenge of building the very first integrated eukaryotic genome database and evolving across 30 years into a global knowledge hub for genetics, functional genomics, and human disease research. The history is organized chronologically, with each section highlighting the central ideas, technical developments, and concrete accomplishments of that period.

Databases, Genetic↗
PubMed2006

Eukaryotic genome size databases.

Three independent databases of eukaryotic genome size information have been launched or re-released in updated form since 2005: the Plant DNA C-values Database (www.kew.org/genomesize/homepage.html), the Animal Genome Size Database (www.genomesize.com) and the Fungal Genome Size Database (www.zbi.ee/fungal-genomesize/). In total, these databases provide freely accessible genome size data for >10,000 species of eukaryotes assembled from more than 50 years' worth of literature. Such data are of significant importance to the genomics and broader scientific community as fundamental features of genome structure, for genomics-based comparative biodiversity studies, and as direct estimators of the cost of complete sequencing programs.

Animals↗
PubMed2003

WiGID: wireless genome information database.

UNLABELLED: WiGID, wireless genome information database, is a new application for mobile internet and can be reached through wireless application protocol (WAP). The main purpose of WiGID is to give easy access to information on completely sequenced genomes. Genome entries in WiGID can be queried by the number of open reading frames (ORFs), genus and species name and year published. Initial search results are linked to information on the full entry. AVAILABILITY: WiGID can be accessed through WAP at http://wigid.cgb.ki.se/index.wml and through the regular internet at http://wigid.cgb.ki.se.

Database Management Systems↗
PubMed1991

Genome mapping databases: data acquisition, storage and access.

The introduction of the genome database to the human gene mapping community in September 1990 heralded the advent of a new generation of databases to serve the needs of the human genome initiative over the coming years. The databases will act as a fulcrum around which the activities of the human genome initiative can be coordinated at an international level.

Animals↗
PubMed2006

AMiGA: the arthropodan mitochondrial genomes accessible database.

UNLABELLED: The Arthropodan Mitochondrial Genomes Accessible database (AMiGA) is a relational database developed to help in managing access to the increasing amount of data arising from developments in arthropodan mitochondrial genomics (136 mitochondrial genomes as of September 2005). The strengths of AMiGA include (1) a more accessible and up-to-date database containing a more comprehensive set of mitochondrial genomes for this phylum, (2) the provision of flexible search options for retrieving detailed information such as bibliographical data, genomic graphics, FASTA sequences and taxonomical status, (3) the possibility of enhanced comparative analyses by multiple alignment of single or concatenated sets of genes, (4) more accurate and updated information resulting from a specific curation process called AMiGA Notes and (5) the possibility of including unpublished sequences in a password-restricted area for comparative analysis with the other sequences stored in the database. AVAILABILITY: http://amiga.cbmeg.unicamp.br CONTACT: lessinger@amiga.cbmeg.unicamp.br SUPPLEMENTARY INFORMATION: Detailed information, including an illustrated tutorial, is available from the above URL.

Animals↗
PubMed2004

The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms.

Currently, the Genomic Threading Database (GTD) contains structural assignments for the proteins encoded within the genomes of nine eukaryotes and 101 prokaryotes. Structural annotations are carried out using a modified version of GenTHREADER, a reliable fold recognition method. The Gen THREADER annotation jobs are distributed across multiple clusters of processors using grid technology and the predictions are deposited in a relational database accessible via a web interface at http://bioinf.cs.ucl.ac.uk/GTD. Using this system, up to 84% of proteins encoded within a genome can be confidently assigned to known folds with 72% of the residues aligned. On average in the GTD, 64% of proteins encoded within a genome are confidently assigned to known folds and 58% of the residues are aligned to structures.

Animals↗
PubMed1996

A graph conceptual model for developing Human Genome Center databases.

We have developed a representation of genome data which has proven itself useful for describing data at a Human Genome Center. Genomic data have a graph-like structure and representing the concepts and relationships of genetics as a graph simplifies the development of databases for genome laboratories. Graphs are a comfortable communication medium for biologists and computer scientists and graph diagrams assist in the development of databases by facilitating the exchange of expertise. We have tailored a graph language for modeling genomic data and describe our process of using graphs to develop genome databases.

Computer Graphics↗
PubMed1999

Genomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wide.

UNLABELLED: GOLD (Genomes On Line Database) is a World Wide Web resource for comprehensive access to information regarding complete and ongoing genome projects around the world. AVAILABILITY: GOLD is based at the University of Illinois at Urbana-Champaign and is available at http://geta.life.uiuc.edu/ approximately nikos/genomes. html. It is also mirrored at the European Bioinformatics Institute at http://www.ebi.ac.uk/research/cgg/genomes.html. CONTACT: genomes@ebi.ac.uk

Databases, Factual↗
PubMed2003

CORG: a database for COmparative Regulatory Genomics.

Sequence conservation in non-coding, upstream regions of orthologous genes from man and mouse is likely to reflect common regulatory DNA sites. Motivated by this assumption we have delineated a catalogue of conserved non-coding sequence blocks and provide the CORG-'COmparative Regulatory Genomics'-database. The data were computed based on statistically significant local suboptimal alignments of 15 kb regions upstream of the translation start sites of, currently, 10 793 pairs of orthologous genes. The resulting conserved non-coding blocks were annotated with EST matches for easier detection of non-coding mRNA and with hits to known transcription factor binding sites. CORG data are accessible from the ENSEMBL web site via a DAS service as well as a specially developed web service (http://corg.molgen.mpg.de) for query and interactive visualization of the conserved blocks and their annotation.

Animals↗