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At least 541 records · Page 30Linked to original sources
PubMed2005

GrainGenes 2.0. an improved resource for the small-grains community.

GrainGenes (http://wheat.pw.usda.gov) is an international database for genetic and genomic information about Triticeae species (wheat [Triticum aestivum], barley [Hordeum vulgare], rye [Secale cereale], and their wild relatives) and oat (Avena sativa) and its wild relatives. A major strength of the GrainGenes project is the interaction of the curators with database users in the research community, placing GrainGenes as both a data repository and information hub. The primary intensively curated data classes are genetic and physical maps, probes used for mapping, classical genes, quantitative trait loci, and contact information for Triticeae and oat scientists. Curation of these classes involves important contributions from the GrainGenes community, both as primary data sources and reviewers of published data. Other partially automated data classes include literature references, sequences, and links to other databases. Beyond the GrainGenes database per se, the Web site incorporates other more specific databases, informational topics, and downloadable files. For example, unique BLAST datasets of sequences applicable to Triticeae research include mapped wheat expressed sequence tags, expressed sequence tag-derived simple sequence repeats, and repetitive sequences. In 2004, the GrainGenes project migrated from the AceDB database and separate Web site to an integrated relational database and Internet resource, a major step forward in database delivery. The process of this migration and its impacts on database curation and maintenance are described, and a perspective on how a genomic database can expedite research and crop improvement is provided.

Breeding↗
PubMed2003

IMGT, the international ImMunoGeneTics information system, http://imgt.cines.fr: the reference in immunoinformatics.

IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr), is a high quality integrated information system specializing in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) and related proteins of the immune system of human and other vertebrates, created in 1989, by the Laboratoire d'ImmunoGénétique Moléculaire (LIGM), at the Université Montpellier II, CNRS, Montpellier, France. IMGT is the global reference in immunogenetics and immunoinformatics and provides a common access to standardized data which include nucleotide and protein sequences, oligonucleotide primers, gene maps, genetic polymorphisms, specificities, 2D and 3D structures. IMGT includes three sequence databases (IMGT/LIGM-DB, IMGT/MHC-DB hosted at EBI, IMGT/PRIMER-DB), one genome database (IMGT/GENE-DB), one 3D structure database (IMGT/3Dstructure-DB), Web resources comprising 8000 HTML pages ("IMGT Marie-Paule page") and interactive tools for sequence (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/Allele-Align, IMGT/PhyloGene) and genome (IMGT/GeneSearch, IMGT/GeneView, IMGT/LocusView) analysis. IMGT data are expertly annotated according to the rules of the IMGT Scientific chart, based on the IMGT-ONTOLOGY concepts. IMGT tools are particularly useful for the analysis of the IG and TR repertoires in physiological normal and pathological situations. IMGT has important applications in medical research (repertoire analysis in autoimmune diseases, AIDS, leukemias, lymphomas, myelomas), biotechnology related to antibody engineering (phage displays, combinatorial libraries) and therapeutic approaches (graft, immunotherapy). IMGT is freely available at http://imgt.cines.fr.

Animals↗
PubMed2003

IMGT, the international ImMunoGeneTics information system, http://imgt.cines.fr.

IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr), is a high quality integrated knowledge resource specializing in immunoglobulins (IG), T cell receptors (TR) and major histocompatibility complexes (MHC) and related proteins of the immune system (RPI) of human and other vertebrates, created in 1989 by LIGM at the Université Montpellier II, CNRS, Montpellier, France. IMGT provides a common access to standardized data which include nucleotide and protein sequences, oligonucleotide primers, gene maps, genetic polymorphisms, specificities, and 2D and 3D structures. IMGT includes five databases (IMGT/LIGM-DB, IMGT/3Dstructure-DB, IMGT/MHC-DB, IMGT/PRIMER-DB, IMGT/GENE-DB) Web resources ('IMGT Marie-Paule page') and interactive tools (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/PhyloGene, IMGT/LocusView, IMGT/GeneView, IMGT/GeneSearch, IMGT/StructureQuery). IMGT data are expertly annotated according to the rules of the IMGT Scientific chart based on IMGTONTOLOGY. IMGT tools are particularly useful for the analysis of the IG and TR repertoires in physiological normal and pathological situations. IMGT has important applications in medical research (autoimmune diseases, AIDS, leukaemias, lymphomas, myelomas), biotechnology related to antibody engineering (phage displays, combinatorial libraries) and therapeutic approaches (graft, immunotherapy). IMGT is freely available at http://imgt.cines.fr.

Animals↗
PubMed2005

A bioinformatics framework for genotype-phenotype correlation in humans with Marfan syndrome caused by FBN1 gene mutations.

Mutations in the human FBN1 gene are known to be associated with the Marfan syndrome, an autosomal dominant inherited multi-systemic connective tissue disorder. However, in the absence of solid genotype-phenotype correlations, the identification of an FBN1 mutation has only little prognostic value. We propose a bioinformatics framework for the mutated FBN1 gene which comprises the collection, management, and analysis of mutation data identified by molecular genetic analysis (DHPLC) and data of the clinical phenotype. To query our database at different levels of information, a relational data model, describing mutational events at the cDNA and protein levels, and the disease's phenotypic expression from two alternative views, was implemented. For database similarity requests, a query model which uses a distance measure based on log-likelihood weights for each clinical manifestation, was introduced. A data mining strategy for discovering diagnostic markers, classification and clustering of phenotypic expressions was provided which enabled us to confirm some known and to identify some new genotype-phenotype correlations.

Computational Biology↗
PubMed2025

GBRAP: A Comprehensive Database and Tool for Exploring Genomic Diversity Across All Domains of Life.

Evolutionary studies require extensive examination of genomic information across all domains of life. Despite the availability of a large number of genomes through GenBank, the effective visualization or comparison of the information they contain is challenging due to many reasons, including their size. We introduce genome-based retrieval and analysis parser, a comprehensive software tool to analyze genome files, and an online database housing an extensive collection of carefully curated, high-quality genome statistics for all the organisms available in the RefSeq database of National Center for Biotechnology Information. Users can either directly search, or select from precategorized groups, the organisms of their choice and retrieve data, and the output is generated as tables containing more than 200 columns of useful genomic information (base counts, GC content, Shannon entropy, codon usage, etc.) separately calculated for different genomic elements (e.g. coding sequences, introns, transfer RNA, ribosomal RNA, noncoding RNA, etc.). The data are independently displayed (if applicable) for each chromosomal, mitochondrial, plastid, or plasmid sequence. All the data can be visualized on the database or downloaded as comma-separated value or Excel files. The genome-based retrieval and analysis parser database is free to access without any registration and is publicly available at http://tacclab.org/gbrap/.

Software↗
PubMed1994

FlyBase--the Drosophila database. The FlyBase Consortium.

FlyBase is a database of genetic and molecular data concerning Drosophila. FlyBase is maintained as a relational database (in Sybase) and is available from the ftp.bio.indiana.edu Gopher server. The scope of FlyBase includes: genes, alleles, aberrations, pointers to sequence data, stock lists, Drosophila workers and bibliographic references.

Alleles↗
PubMed1996

FlyBase: the Drosophila database.

FlyBase is a database of genetic and molecular data concerning Drosophila. FlyBase is maintained as a relational database (in Sybase). The scope of FlyBase includes: genes, alleles (and phenotypes), aberrations, pointers to sequence data, clones, stock lists, Drosophila workers and bibliographic references. FlyBase is also available on CD-ROM for Macintosh systems (Encyclopaedia of Drosophila).

Alleles↗
PubMed1997

FlyBase: a Drosophila database. The FlyBase consortium.

FlyBase is a database of genetic and molecular data concerning Drosophila. FlyBase is maintained as a relational database (in Sybase) and is made available as html documents and flat files. The scope of FlyBase includes: genes, alleles (and phenotypes), aberrations, transposons, pointers to sequence data, clones, stock lists, Drosophila workers and bibliographic references. The Encyclopedia of Drosophila is a joint effort between FlyBase and the Berkeley Drosophila Genome Project which integrates FlyBase data with those from the BDGP.

Animals↗
PubMed1998

FlyBase: a Drosophila database.

FlyBase (http://flybase.bio.indiana.edu/) is a comprehensive database of genetic and molecular data concerning Drosophila . FlyBase is maintained as a relational database (in Sybase) and is made available as html documents and flat files. The scope of FlyBase includes: genes, alleles (with phenotypes), aberrations, transposons, pointers to sequence data, gene products, maps, clones, stock lists, Drosophila workers and bibliographic references.

Animals↗
PubMed2006

Genes, race, and population: avoiding a collision of categories.

A wide array of federal mandates have a profound impact on the use of racial and ethnic categories in biomedical research, clinical practice, product development, and health policy. Current discussions over the appropriate use of racial and ethnic categories in biomedical contexts have largely focused on the practices of individual researchers. By contrast, our discussion focuses on relations between the daily practices of biomedical professionals and federal regulatory mandates. It draws upon the legal doctrine of equal protection to move beyond such debates and to propose guidelines to address the structural forces imposed by federal regulations that mandate how data about race and ethnicity are used in biomedical research. It offers a framework to manage the tension involved in using existing federally mandated categories of race and ethnicity alongside new scientific findings about human genetic variation.

Biomedical Research↗
PubMed2003

IMGT-ONTOLOGY for immunogenetics and immunoinformatics.

IMGT, the international ImMunoGeneTics information system(R) (http://imgt.cines.fr), is a high quality integrated knowledge resource specializing in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) and related proteins of the immune system (RPI) of human and other vertebrates, created in 1989, by the Laboratoire d'ImmunoGenetique Moleculaire LIGM. IMGT provides a common access to standardized data which include nucleotide and protein sequences, oligonucleotide primers, gene maps, genetic polymorphisms, specificities, 2D and 3D structures. IMGT consists of several sequence databases (IMGT/LIGM-DB, IMGT/MHC-DB, IMGT/PRIMER-DB), one genome database (IMGT/GENE-DB) and one three-dimensional structure database (IMGT/3Dstructure-DB), interactive tools for sequence analysis (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/PhyloGene, IMGT/Allele-Align), for genome analysis (IMGT/GeneSearch, IMGT/GeneView, IMGT/LocusView) and for 3D structure analysis (IMGT/StructuralQuery), and Web resources ("IMGT Marie-Paule page") comprising 8000 HTML pages. IMGT other accesses include SRS, FTP, search by BLAST, etc. By its high quality and its easy data distribution, IMGT has important implications in medical research (repertoire in autoimmune diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research, genome diversity and genome evolution studies of the adaptive immune responses, biotechnology related to antibody engineering (scFv, phage displays, combinatorial libraries) and therapeutical approaches (grafts, immunotherapy). IMGT is freely available at http://imgt.cines.fr.

Animals↗
PubMed2003

An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences.

MOTIVATION: Sequence databases encode a wealth of information needed to develop improved vaccination and treatment strategies for the control of HIV and other important pathogens. To facilitate effective utilization of these datasets, we developed a user-friendly GDE-based LINUX interface that reduces input/output file formatting. DESIGN AND RESULTS: GDE was adapted to the Linux operating system, bioinformatics tools were integrated with microbe-specific databases, and up-to-date GDE menus were developed for several clinically important viral, bacterial and parasitic genomes. Each microbial interface was designed for local access and contains Genbank, BLAST-formatted and phylogenetic databases. AVAILABILITY: GDE-Linux is available for research purposes by direct application to the corresponding author. Application-specific menus and support files can be downloaded from (http://www.bioafrica.net).

Database Management Systems↗