copied from Nucleic Acids Research, 2005, Vol. 33, Database issue (link directs to table of contents with many original papers on the below mentioned databases)
back to Database resources and links

No.b Database_name_________ Full_name_and/or_description____________________ URL 1. Nucleotide Sequence Databases 1.1. International Nucleotide Sequence Database Collaboration 1 DDBJ—DNA Data Bank of Japan All known nucleotide and protein sequences http://www.ddbj.nig.ac.jp 2 EMBL Nucleotide Sequence Database All known nucleotide and protein sequences http://www.ebi.ac.uk/embl.html 3 GenBank® All known nucleotide and protein sequences http://www.ncbi.nlm.nih.gov/Entrez 1.2. DNA sequences: genes, motifs and regulatory sites 1.2.1. Coding and coding DNA 403 ACLAME A classification of genetic mobile elements http://aclame.ulb.ac.be/ 30 CUTG Codon usage tabulated from GenBank http://www.kazusa.or.jp/codon/ 480 Genetic Codes Genetic codes in various organisms and organelles http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi 668 Entrez Gene Gene-centered information at NCBI http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene 495 HERVd Human endogenous retrovirus database http://herv.img.cas.cz 687 Hoppsigen Human and mouse homologous processed pseudogenes http://pbil.univ-lyon1.fr/databases/hoppsigen.html 294 Imprinted Gene Catalogue Imprinted genes and parent-of-origin effects in animals http://www.otago.ac.nz/IGC 512 Islander Pathogenicity islands and prophages in bacterial genomes http://www.indiana.edu/~islander 343 MICdb Prokaryotic microsatellites http://www.cdfd.org.in/micas 707 NPRD Nucleosome positioning region database http://srs6.bionet.nsc.ru/srs6/ 47 STRBase Short tandem DNA repeats database http://www.cstl.nist.gov/div831/strbase/ 5 TIGR Gene Indices Organism-specific databases of EST and gene sequences http://www.tigr.org/tdb/tgi.shtml 48 Transterm Codon usage, start and stop signals http://uther.otago.ac.nz/Transterm.html 6 UniGene Non-redundant set of eukaryotic gene-oriented clusters http://www.ncbi.nlm.nih.gov/UniGene/ 320 UniVec Vector sequences, adapters, linkers and primers used in DNA cloning, can be used to check for vector contamination http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html 302 VectorDB Characterization and classification of nucleic acid vectors http://genome-www2.stanford.edu/vectordb/ 305 Xpro Eukaryotic protein-encoding DNA sequences, both intron-containing and intron-less genes http://origin.bic.nus.edu.sg/xpro/ 1.2.2. Gene structure, introns and exons, splice sites 414 ASAP Alternative spliced isoforms http://www.bioinformatics.ucla.edu/ASAP 28 ASD Alternative splicing database at EBI, includes three databases AltSplice, AltExtron and AEdb http://www.ebi.ac.uk/asd 10 ASDB Alternative splicing database: protein products and expression patterns of alternatively spliced genes http://hazelton.lbl.gov/~teplitski/alt 639 ASHESdb Alternatively spliced human genes by exon skipping database http://sege.ntu.edu.sg/wester/ashes/ 450 EASED Extended alternatively spliced EST database http://eased.bioinf.mdc-berlin.de/ 667 ECgene Genome annotation for alternative splicing http://genome.ewha.ac.kr/ECgene/ 631 EDAS EST-derived alternative splicing database http://www.ig-msk.ru:8005/EDAS/ 34 ExInt Exon–intron structure of eukaryotic genes http://sege.ntu.edu.sg/wester/exint/ 36 HS3D Homo sapiens splice sites dataset http://www.sci.unisannio.it/docenti/rampone/ 238 Intronerator Alternative splicing in C.elegans and C.briggsae http://www.cse.ucsc.edu/~kent/intronerator/ 46 SpliceDB Canonical and non-canonical mammalian splice sites http://www.softberry.com/berry.phtml?topic=splicedb&group=data&subgroup=spldb 746 SpliceInfo Modes of alternative splicing in human genome http://140.115.50.96/SpliceInfo/ 580 SpliceNest A tool for visualizing splicing of genes from EST data http://splicenest.molgen.mpg.de/ 1.2.3. Transcriptional regulator sites and transcription factors 231 ACTIVITY Functional DNA/RNA site activity http://wwwmgs.bionet.nsc.ru/mgs/systems/activity/ 31 DBTBS Bacillus subtilis promoters and transcription factors http://dbtbs.hgc.jp/ 663 DoOP Database of orthologous promoters: chordates and plants http://doop.abc.hu/ 106 DPInteract Binding sites for E.coli DNA-binding proteins http://arep.med.harvard.edu/dpinteract 33 EPD Eukaryotic promoter database http://www.epd.isb-sib.ch 494 HemoPDB Hematopoietic promoter database: transcriptional regulation in hematopoiesis http://bioinformatics.med.ohio-state.edu/HemoPDB 516 JASPAR PSSMs for transcription factor DNA-binding sites http://jaspar.cgb.ki.se 700 MAPPER Putative transcription factor binding sites in various genomes http://bio.chip.org/mapper 40 PLACE Plant cis-acting regulatory DNA elements http://www.dna.affrc.go.jp/htdocs/PLACE 41 PlantCARE Plant promoters and cis-acting regulatory elements http://intra.psb.ugent.be:8080/PlantCARE/ 563 PlantProm Plant promoter sequences for RNA polymerase II http://mendel.cs.rhul.ac.uk/ 566 PRODORIC Prokaryotic database of gene regulation networks http://prodoric.tu-bs.de/ 42 PromEC E.coli promoters with experimentally identified transcriptional start sites http://bioinfo.md.huji.ac.il/marg/promec 246 SELEX_DB DNA and RNA binding sites for various proteins, found by systematic evolution of ligands by exponential enrichment http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/ 227 TESS Transcription element search system http://www.cbil.upenn.edu/tess 756 TRACTOR db Transcription factors in gamma-proteobacteria database http://www.tractor.lncc.br/ 345 TRANSCompel Composite regulatory elements affecting gene transcription in eukaryotes http://www.gene-regulation.com/pub/databases.html#transcompel 340 TRANSFAC Transcription factors and binding sites http://transfac.gbf.de/TRANSFAC/index.html 757 TRED Transcriptional regulatory element database http://rulai.cshl.edu/tred 49 TRRD Transcription regulatory regions of eukaryotic genes http://www.bionet.nsc.ru/trrd/

^a Each database is shown in the list only once, often in a category that was arbitrarily chosen among two or three appropriate ones. In the online version of this list at the NAR website (http://nar.oupjournals.org/), a database can be listed under two categories.

^b Accession number of the database in the online list; can be used to view the database summary, e.g. http://www3.oup.co.uk/nar/database/summary/1 shows the summary for DDBJ.