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You are here Biopharmaceutical Glossary Homepage > Informatics > Biopharmaceutical Databases directory
BioPharmaceutical Databases directory Related glossaries include Bioinformatics (see definitions of databases and various narrower terms), Chemoinformatics This webpage isn't totally up to date. Life science databases Wikipedia https://en.wikipedia.org/wiki/List_of_biological_databases NCBI Handbook, guide National Center
for Biotechnology Information, NLM, NIH, 2013 Databases and other NCBI
Resources
https://www.ncbi.nlm.nih.gov/books/NBK143764/
Molecular Cellular and Developmental Biology databases, University of
Michigan Library Research guide
https://guides.lib.umich.edu/molecular Bibliographic/journals,
e-books and tutorials ************************************************************************** This is not a comprehensive catalog of databases. Both public and proprietary databases are included. Many proprietary databases may make special arrangements for academic users. Please consult individual websites for details. The dividing line between databases, software and integrated systems gets blurrier all the time. DATABASES 2D PAGE databases index http://au.expasy.org/ch2d/2d-index.html 3Dee Database of Protein Domain Definitions, EBI, UK http://www.compbio.dundee.ac.uk/3Dee/ Structural domain definitions for all protein chains in the Brookhaven Protein Databank (PDB) that have 20 or more residues and are not theoretical models [listed here]. In addition, the domains have been clustered on sequence similarity and structural similarity. The resulting families are stored as a hierarchy. ALFRED Allele Frequency Database, Kidd Lab, Yale University, US http://alfred.med.yale.edu/alfred/index.asp Amino Acid Index AAI, GenomeNet, Japan http://www.genome.ad.jp/dbget/aaindex.html An amino acid index is a set of 20 numerical values representing any of the different physicochemical and biological properties of amino acids. The AAindex1 section of the Amino Acid Index Database is a collection of published indices together with the result of cluster analysis using the correlation coefficient as the distance between two indices. ArrayExpress, EBI, UK http://www.ebi.ac.uk/arrayexpress/ A public repository for microarray based gene expression data. Currently the EBI is establishing a pilot database containing microarray gene expression data that are available publicly. BioModels Database; BioModels.net initiative, a collaboration amongst the SBML Team (USA), the EMBL-EBI (United-Kingdom), the Systems Biology Group of the Keck Graduate Institute (USA), the Systems Biology Institute (Japan), and JWS Online at the Stellenbosch University (South Africa). http://www.ebi.ac.uk/biomodels/ Annotated published models.... an effort to develop a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. BIOSIS Biological Abstracts, https://en.wikipedia.org/wiki/BIOSIS_Previews Bibliographic index to biological literature. Berkeley Drosophila Genome Project BDGP, http://www.fruitfly.org/ UC-Berkeley, US Curated annotated informatics database from the Berkeley and European Drosophila genome projects, with annotations from the literature, comparative sequence analysis and the FlyBase research community. Biochemical Pathways, https://web.expasy.org/pathways/ Originally from Boehringer Mannheim GmbH https://www.roche.com/sustainability/philanthropy/science_education/pathways.htm BioExpress See GeneExpress BioMagRes, Univ. of Wisconsin-Madison, US http://www.bmrb.wisc.edu/ Contains NMR chemical shifts derived from proteins and peptides, reference data, amino acid sequence information, and data describing the source of the protein and the conditions used to study the protein. In constructing the database, proteins and larger peptides have been given priority. Shift assignments for hemes, cofactors, and substrates of a protein are also included, when they are reported as part of a complex. BioMedCentral (UK) http://www.biomedcentral.com/home/ Publisher of journals covering all areas of biology and medicine. We provide free access to peer- reviewed research articles and subscription- based access to reviews, commentaries and other information services CATH Protein Structure Classification, University College, London, UK http://www.cathdb.info/ Protein domains classified into superfamilies. CDD Conserved Domain Database, NCBI, US http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml Database and search service. currently contains domains derived from two popular collections, Smart and Pfam, plus contributions from colleagues at NCBI. The source databases also provide descriptions and links to citations. Since conserved domains correspond to compact structural units, CDs contain links to 3D-structure via Cn3D whenever possible. CGAP Cancer Gene Anatomy Project, NCBI, US http://www.ncbi.nlm.nih.gov/ncicgap/ An interdisciplinary program established and administered by the National Cancer Institute to generate the information and technological tools needed to decipher the molecular anatomy of the cancer cell. CGAP is divided into five complementary Initiatives, each with its own goals, informatics tools and resources. Chemical Abstracts CA http://www.cas.org/ Bibliographic index to the chemical literature. COG Clusters of Orthologous Groups of Proteins, NCBI, US. http://www.ncbi.nlm.nih.gov/COG/ Delineated by comparing protein sequences encoded in 21 complete genomes, representing 17 major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. Conserved Domain Database CDD, NCBI, US http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml currently contains domains derived from two popular collections, Smart and Pfam, plus contributions from colleagues at NCBI. The source databases also provide descriptions and links to citations. Since conserved domains correspond to compact structural units, CDs contain links to 3D-structure via Cn3D whenever possible. CrossRef http://www.crossref.org Publishers International Linking Association 77 publishers of over 4,780 journals. Database of Macromolecular Movements, Molecular Biophysics and Biochemistry, Yale Univ., US http://bioinfo.mbb.yale.edu/MolMovDB/ This describes the motions that occur in proteins and other macromolecules, particularly using movies. Associated with it are a variety of free software tools and servers for structural analysis. M Gerstein & WG Krebs (1998). Nuc. Acid. Res. 26:4280-4290 DBGET/LinkDB, GenomeNet, Institute for Chemical Research, Kyoto University, Japan http://www.genome.ad.jp/dbget/ Integrated database retrieval system, currently supports the following databases and gene catalogs: nucleic acid sequences: GenBank, EMBL protein sequences: SWISS- PROT, PIR, PRF, PDB, STR, 3D structures: PDB, sequence motifs: PROSITE, EPD, TRANSFAC, enzyme reactions: LIGAND, metabolic pathways: PATHWAY, amino acid mutations: PMD, amino acid indices: AAindex, genetic diseases: OMIM, literature: LITDB, Medline, gene catalogs: E. coli, H. influenzae, M. genitalium, M. pneumoniae, M. jannaschii, Synechocystis, S. cerevisiae, cross reference EMBL and GenBank dbSNP, NCBI http://www.ncbi.nlm.nih.gov/SNP/ Uses "looser variation" definition for SNPs (no requirement or assumption about minimum allele frequencies or the polymorphisms…Short deletion and insertion polymorphisms, and microsatellite repeats, as well as SNPs are included. Disease causing clinical mutations, as well as neutral polymorphisms, are also in scope. [dbSNP FAQ] dbSTS, NCBI http://www.ncbi.nlm.nih.gov/dbSTS/ A subset of GenBank, with sequence and mapping data on short genomic landmark sequences (STSs). More comprehensive annotation than in GenBank and regularly updated with BLAST. DDBJ
DNA DataBank of Japan Shares information daily with EMBL
and GenBank. http://www.ddbj.nig.ac.jp/
DOGS Database of Genome Sizes Center for Biological Sequence Analysis, Technical University Denmark http://www.cbs.dtu.dk/databases/DOGS/index.html A comprehensive list of (estimated) genome sizes for different organisms. The purpose of this database is to provide such a list. The ultimate goal is to compile a list of all the known organisms and their respective genome sizes. Both the completed and estimated genomes are listed. The estimated genome sizes are given for both the organisms currently being sequenced and those for which no sequencing programme is in progress. DOTS Database of Transcribed Sequences, Univ. of Pennsylvania, US. Has been superseded by http://www.allgenes.org/ which combines data from DOTS and the Genome Channel (ORNL). DrugBank: A unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains nearly 4300 drug entries including >1,000 FDA-approved small molecule drugs, 113 FDA-approved biotech (protein/peptide) drugs, 62 nutraceuticals and >3,000 experimental drugs. Additionally, more than 6,000 protein (i.e. drug target) sequences are linked to these drug entries. Each DrugCard entry contains more than 80 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data. DrugBank Wishart DS et al., DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 2006 1;34 EMBASE Excerpta Medica http://www.embase.com/home Bibliographic index to biomedical and pharmacological literature. EMBL (European Molecular Biology Laboratory: Main laboratory is in Heidelberg, Germany, with outstations in Hamburg, Grenoble, France (access to high powered instruments for structure studies) and Hinxton, UK (bioinformatics). Supported by 14 European countries and Israel, shares data daily with DDBJ and GenBank. http://www.embl-heidelberg.de/ ENCODE ENCyclopedia of DNA Elements, NHGRI http://www.genome.gov/10005107 Before the best use of the information contained in the [human genome] sequence can be made, the identity and precise location of all of the protein- encoding and non- protein- encoding genes will have to be determined. The identity of other functional elements encoded in the DNA sequence, such as promoters and other transcriptional regulatory sequences, along with determinants of chromosome structure and function, such as origins of replication, also remain largely unknown. A comprehensive encyclopedia of all of these features is needed to fully utilize the sequence to better understand human biology, to predict potential disease risks, and to stimulate the development of new therapies to prevent and treat these diseases. Entrez Genomes, NCBI, US http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome Entrez Nucleotides, NCBI, US http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide A collection of sequences from several sources, including GenBank, RefSeq, and PDB. The number of bases grows at an exponential rate. Entrez Programming Utilities (E-utilities) are a set of eight server-side programs that provide a stable interface into the Entrez query and database system at the National Center for Biotechnology Information (NCBI). The E-utilities use a fixed URL syntax that translates a standard set of input parameters into the values necessary for various NCBI software components to search for and retrieve the requested data. The E-utilities are therefore the structured interface to the Entrez system, which currently includes 38 databases covering a variety of biomedical data, including nucleotide and protein sequences, gene records, three-dimensional molecular structures, and the biomedical literature. http://www.ncbi.nlm.nih.gov/books/NBK25501/ Entrez Proteins, NCBI, US http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?db=Protein The protein entries in the Entrez search and retrieval system have been compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq. ENZYME, ExPASy, Switzerland http://au.expasy.org/enzyme/ Enzyme nomenclature database EpoDB Erythropoiesis database, CBIL (Computational Biology & Informatics Lab), Univ. of Pennsylvania, US http://www.cbil.upenn.edu/EpoDB/index.html A database of genes that relate to vertebrate red blood cells. It includes DNA sequence, structural features, protein information, gene expression information and transcription factor binding sites. ExPASy (Expert Protein Analysis System), Swiss Institute of Bioinformatics, Switzerland http://au.expasy.org/ Proteomics server Express DB, George Church Lab, Harvard Medical School, US http://arep.med.harvard.edu/ExpressDB/ A relational database for maintaining yeast RNA expression data. It is intended as a demonstration of how such data can be managed, and of the benefits such management confers. As of July, 1999, over 17.5 million pieces of information have been loaded into ExpressDB deriving from 11 source studies. The EXD web query system allows data from multiple source studies to be retrieved to user specifications and collated by ORF name. FlyBase See Berkeley Drosophila GenAtlas Univ. Rene Descartes, France http://genatlas.org/ Genes, phenotypes and markers for humans. GenBank:, NCBI, US http://www.ncbi.nlm.nih.gov/Genbank/ NIH genetic sequence database, annotated collection of all publicly available DNA sequence Mirrored at EMBL and DDBJ. Currently estimated (early 2000) that over 2 million bases are deposited here each day. This growth will only accelerate in the future. Began in the 1980’s by DOE. Cross reference DDBJ and EMBL. See also Sequencing Glossary. GeneCards, Weizmann Institute, Israel http://www.genecards.org/index.shtml Numerous mirrored sites, database of human genes, their products and their involvement in diseases. It offers concise information about the functions of all human genes that have an approved symbol, as well as selected others. Gene Census system, Yale University, US http://bioinfo.mbb.yale.edu/genome/ Comprehensive statistical accounting of protein structural features in genomes and sequence databanks. Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo/ A high- throughput gene expression / molecular abundance data repository, as well as a curated, online resource for gene expression data browsing, query and retrieval. Gene Map of the Human Genome, International RH Mapping Consortium http://www.ncbi.nlm.nih.gov/genemap99/ Includes locations of more than 30,000 genes and provides an early glimpse of some of the most important pieces of the genome. GGEG Global Gene Expression Database, MD Anderson Cancer Center Human mRNA sequence data specific to the RAGE and SAGE techniques, general mRNA information. GPCRDB: Information system for G- Protein Coupled Receptors (GPCRs),
Univ. of Nijmegen, UCSF, EBI, IPSI, Leiden/ Amsterdam Center for Drug
Research, SWISS- PROT, tinyGrap http://gpcrdb.org/
GSDB See Genome Sequence DataBase GSS Genome Survey Sequences, NCBI, US http://www.ncbi.nlm.nih.gov/dbGSS/ The GSS division of GenBank is similar to the EST division, except that its sequences are genomic in origin, rather than cDNA (mRNA). The GSS division contains (but is not limited to) the following types of data: random "single pass read" genome survey sequences, cosmid/BAC/YAC end sequences, exon trapped genomic sequences, Alu PCR sequences. GXD: Gene Expression Database, Jackson Laboratory, US http://www.informatics.jax.org/mgihome/GXD/gxdgen.shtml#concept Gene expression data on the laboratory mouse. Highwire Press, Stanford Univ., US http://highwire.org Free (and fee-based), full- text science journals. HOMOLOGENE, NCBI, US https://www.ncbi.nlm.nih.gov/homologene/ A homology resource which includes both curated and calculated orthologs and homologs for genes represented in UniGene and LocusLink for human, mouse, rat, and zebrafish. The curated orthologs include ortholog gene pairs reported in the Mouse Genome Database (MGD) at the Jackson Laboratory, the Zebrafish Information (ZFIN) database at the University of Oregon, and in published reports. The calculated orthologs and homologs are the result of nucleotide sequence comparisons between all UniGene clusters for each pair of organisms. These orthologs and homologs are considered putative since they are based only on sequence comparisons. HOVERGEN Homologous Vertebrate Genes Database, PBIL (Pôle Bio-Informatique Lyonnais, Univ. Lyons, France http://biom3.univ-lyon1.fr/databases/hovergen.html A database of homologous vertebrate genes, structured under ACNUC sequence database management system. It allows one to select sets of homologous genes among vertebrate species, and to visualize multiple alignments and phylogenetic trees. Thus HOVERGEN is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies. More generally, HOVERGEN gives an overall view of what is known about a peculiar [particular?] gene family. The database itself contains all vertebrate sequences from GenBank (except ESTs), with some data corrected, clarified or completed (notably to address the problem of redundancy). Homologous coding sequences have been classified in gene families and protein multiple alignments and phylogenetic trees have been computed for each family. Sequences and related information have been structured in an ACNUC database. The database is updated every four months HTGS High Throughput Genomic Sequences, NCBI, US http://www.ncbi.nlm.nih.gov/HTGS/ created to accommodate a growing need to make 'unfinished' genomic sequence data rapidly available to the scientific community. It was done in a coordinated effort between the three International Nucleotide Sequence databases: DDBJ, EMBL, and GenBank. The HTG division contains 'unfinished' DNA sequences generated by the high-throughput sequencing centers. Sequence data in this division are available for BLAST homology searches against either the "htgs" database or the "month" database, which includes all new submissions for the prior month. The HTG division of GenBank was recently described in a [1997 Genome Research 7(10) article by Ouellette and Boguski. HUGE Human Unidentified Gene Encoded Large Proteins, Kazuza DNA Research Institute, Japan http://www.kazusa.or.jp/huge/The HUGE protein database has been created to publicize the fruits of our Human cDNA project at the Kazusa DNA Research Institute. In this project, we plan to sequence and analyze long (>4 kb) human cDNAs and to establish methods by using the sequence data how to predict the primary structure of proteins of various biological activities. Currently, we focus on the analysis of cDNA clones encoding particularly large proteins (>50 kDa). The basic concept underlying our project and the strategies employed have been described elsewhere (Ohara et al., 1997). Our HUGE protein database contains various types of information derived from the predicted primary structure data of newly identified human proteins Human Mouse Homology Map, NCBI, US http://www.ncbi.nlm.nih.gov/Homology/ Map is now being computed by integrating orthologs curated by the Mouse Genome Database with putative orthologs identified by sequence homology. This version of the Human-Mouse Homology map also differs from the previous Davis map by including several new features: reporting representative STS associated with the loci in the map and linked to the dbSTS pages, linking human cytogenetic locations to NCBI's MapViewer, providing alignments of representative sequences via BLAST2 , and linking gene symbols to LocusLink IXDB Integrated Chromosome X DataBase, Max Planck Institut, Berlin, Germany http://www.molgen.mpg.de/~xteam/ The purpose of IXDB is to provide an integrated view of the X chromosome mapping field. Ultimately this will allow the construction of an integrated map that will take into account all the data generated by the community, including physical, genetic, transcript and sequence information. This implies acquiring, understanding and formatting an enormous amount of experimental results and can only be accomplished progressively. We have chosen to start the integration process with YAC maps generated by the community. These provide the basis for future higher resolution physical maps, as well as emerging transcript and sequence maps. The current content of IXDB therefore reflects this situation, with the emphasis placed on YAC mapping data. Due to their immediate value, IXDB has also started to systematically include bacterial clone contig maps and EST data. Currently IXDB does not store sequence data, although links to nucleic sequence databases are provided. KEGG Pathway Database, http://www.genome.ad.jp/kegg/ Links to pathway and other databases (metabolic and regulatory) http://www.genome.jp/kegg/pathway.html See also note on KEGG under Metabolic engineering glossary pathways LIGAND database, Institute for Chemical Research, Kyoto Univ. Japan http://www.genome.ad.jp/dbget-bin/www_bfind?ligand Enzymes, compounds and reactions. Mammalian Gene Collection, NCBI, US http://mgc.nci.nih.gov/ The goal of the Mammalian Gene Collection (MGC) is to provide a complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for human and mouse. The MGC is an NIH initiative that supports the production of cDNA libraries, clones and sequences. Medline See PubMed MGD See Mouse Genome Database Mitelman DataBase of Chromosome Aberrations in Cancer, CGAP, NCI, US http://cgap.nci.nih.gov/Chromosomes/Mitelman relates chromosomal aberrations to tumor characteristics, based either on individual cases or associations. All the data have been manually culled from the literature by Felix Mitelman, Bertil Johansson, and Fredrik Mertens. MITOMAP, Emory Univ., US http://www.mitomap.org/ A human mitochondrial genome database. A compendium of polymorphisms and mutations of the human mitochondrial DNA.
Mouse Atlas and Gene Expression Database,
Human Genetics Unit, MRC
Medical Research Council, Edinburgh, UK http://genex.hgu.mrc.ac.uk/
Not yet available 11/2/00 A digital atlas of mouse development and database
to be a resource for spatially mapped data such as in situ gene expression
and cell lineage. The project is in collaboration with the Department of
Anatomy, University of Edinburgh. The gene expression database is being
developed as part of the Mouse Gene Expression Information Resource (MGEIR)
in collaboration with the Jackson Laboratory, USA. Mouse Genome Database MGD See Mouse Genome Informatics Mouse Genome Informatics, Jackson Laboratory, US http://www.informatics.jax.org/ international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Mouse Phenome Database, Jackson Labs, US. https://phenome.jax.org/ A collection of baseline phenotypic data on commonly used and genetically diverse inbred mouse strains through a coordinated international effort. Nucleic Acids Database NDB, Rutgers Univ., US http://ndbserver.rutgers.edu/ Assembles and distributes structural information about nucleic acids. See also Protein Data Bank PDB Nucleotide Database https://www.ncbi.nlm.nih.gov/nucleotide As of December 1, 2018, all records from the databases for Expressed Sequence Tags (EST) and Genome Survey Sequences (GSS) will reside in NCBI’s Nucleotidedatabase OMIM, Online Mendelian Inheritance in Man, NCBI, US https://www.ncbi.nlm.nih.gov/omim https://secure.jhu.edu/form/OMIM ooTFD object oriented Transcription factors and gene expression, Institute for Transcriptional Informatics IFTII, US http://www.ifti.org/cgi-bin/ifti/ootfd.pl A successor to TFD (Transcription Factors Database), now referred to as rTFD (relational Transcription Factors Database). ooTFD has been implemented in a number of object-oriented database management systems, including ROL (Rule- based Object Language), MOOD (Materials object- oriented database), and the pure java object database ozone. PDB Protein Data Bank, Research Collaboratory for Structural Bioinformatics http://www.rcsb.org/ 3D macromolecular structural data. Incorporates NDB Nucleic Acid Database Project, Rutgers. PEDB Prostate ESTs, Fred Hutchinson Cancer Research Center, US http://www.pedb.org/ A curated relational database and suite of analysis tools designed for the study of prostate gene expression in normal and disease states. Expressed Sequence Tags (ESTs) and full-length cDNA sequences derived from more than 40 human prostate cDNA libraries are maintained and represent a wide spectrum of normal and pathological conditions. Pfam https://pfam.xfam.org/ a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs) PIR Protein Information Resource, NBRF, Georgetown Univ. Medical Center, US http://pir.georgetown.edu/pirwww/ The Protein Information Resource (PIR), in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japanese International Protein Sequence Database (JIPID) maintains the PIR- International Protein Sequence Database --- a comprehensive, annotated, and non- redundant protein sequence database in which entries are classified into family groups and alignments of each group are available. PROSITE, Swiss Institute of Bioinformatics http://au.expasy.org/prosite/ A database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs PubMed Central, NCBI http://www4.ncbi.nlm.nih.gov/PubMed/ Medline Rat Genome Database See RGD RefSeq Reference Sequences, NCBI, US http://www.ncbi.nlm.nih.gov/RefSeq/ Aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for major research organisms. RefSeq standards serve as the basis for medical, functional, and diversity studies; they provide a stable reference for gene identification and characterization, mutation analysis, expression studies, polymorphism discovery, and comparative analyses. RefSeqs are used as a reagent for the functional annotation of some genome sequencing projects, including those of human and mouse. Research Collaboratory for Structural Bioinformatics RCSB See Protein DataBank RGD Rat Genome Database, Medical College of Wisconsin, US http://rgd.mcw.edu/ is the [Goal is] establishment of a Rat Genome Database, to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community. A secondary, but critical goal is to provide curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data. Saccharomyces Genome Deletion
Project http://sequence-www.stanford.edu/group/yeast_deletion_project/deletions3.html SGD Saccharomyces Genome Database, Stanford University http://www.yeastgenome.org/ Structure https://www.ncbi.nlm.nih.gov/structure Three dimensional structures provide a wealth of information on the biological function and the evolutionary history of macromolecules. They can be used to examine sequence-structure-function relationships, interactions, active sites and more. SWISS 2D PAGE, Swiss Institute of Bioinformatics http://au.expasy.org/ch2d/ Data on proteins identified on various 2-D PAGE reference maps. SWISS 3D Image, ExPASy, Switzerland http://au.expasy.org/sw3d/ An image database which strives to provide high quality pictures of biological macromolecules with known three- dimensional structure. The database contains mostly images of experimentally elucidated structures, but also provides views of well accepted theoretical protein models. SWISS-MODEL Repository, Swiss Institute of Bioinformatics and Biozentrum, Basel http://swissmodel.expasy.org/repository/ A database of annotated three- dimensional comparative protein structure models generated by the fully automated homology- modelling pipeline SWISS- MODEL. SWISS-PROT, ExPASy (Expert Protein Analysis System) Swiss Institute of Bioinformatics A curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. See UniProt. Taxonomy, NCBI, US See Nomenclature UniGene, NCBI, US http://www.ncbi.nlm.nih.gov/UniGene/index.html An experimental system for automatically partitioning GenBank sequences into a non- redundant set of gene- oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location. Well- characterized genes and ESTs. UNI-PROT Knowledgebase Universal Protein Resource, http://www.uniprot.org/ .a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. SWISS PROT, TrEMBL, UniRef, UniParc, Proteomes UniVec, NCBI, US http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html A database that can be used to quickly identify segments within nucleic acid sequences which may be of vector origin (vector contamination) ... In addition to vector sequences, UniVec also contains sequences for those adapters, linkers and primers commonly used in the process of cloning cDNA or genomic DNA. V Base: the database of human antibody genes, Centre for Protein Engineering, Medical Research Council, UK http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html A system for quickly identifying segments of a nucleic acid sequence that may be of vector origin. NCBI developed VecScreen to combat the problem of vector contamination in public sequence databases. Software BLAST (Basic Local Alignment Search Tool): finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.. https://blast.ncbi.nlm.nih.gov/Blast.cgi See also Sequencing glossary Cn3D http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml A helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service. FASTA: Software program, from the University of Virginia, used to scan a protein or DNA sequence library for similar sequences. https://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml See also Sequencing
GRAIL site updates major,
Broad Institute,
https://software.broadinstitute.org/mpg/grail/faq.html
The GRAIL (Gene
Recognition and Assembly Internet Link) program for exon prediction was
originally described in 1991 by Uberacher and Mural (Proc Natl Acad Sci
USA). For years, along with GENSCAN (Burge & Karlin, J. Mol Biol. 1997),
it was widely cited and utilized for defining coding regions within the
genome. Until 2005 it developed and supported by the Oak Ridge National
Laboratory - since then it has been unavailable. We apologize for any
confusion this might have caused. GRAIL: Genome Recognition and Assembly Internet Link was at Oak Ridge National Lab. MedMiner now Miner suite of bioinformatics software https://discover.nci.nih.gov/ ORF Finder, NCBI, US https://www.ncbi.nlm.nih.gov/orffinder/ Gene prediction. Protein Explorer http://www.umass.edu/microbio/chime/explorer/ Supersedes RasMol. RasMol homepage [Macromolecular structure viewer] See Protein Explorer which is now recommended as easier to use and more powerful than RasMol. SEQUEST
http://fields.scripps.edu/yates/wp/?page_id=17
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