The Molecular Biology Database Collection: an updated compilation of biological database resources

Abstract

The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists’ attention to high-quality databases that are available throughout the world, rather than just be a lengthy listing of all available databases. As such, this up-to-date listing is intended to serve as the initial point from which to find specialized databases that may be of use in biological research. The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches. Short, searchable summaries of each of the databases included in the Collection are available through the Nucleic Acids Research Web site, at http://www.nar.oupjournals.org.

With the advent of the new millennium, the scientific community marked a significant milestone in the study of biology—the completion of the ‘working draft’ of the human genome (1). Amongst much fanfare, the completion of the working draft was announced by President Clinton at a White House ceremony on June 26, 2000 (http://www.whitehouse.gov/WH/New/html/20000626.html). This announcement signaled that the majority of biological and biomedical research would now be conducted in a ‘sequence-based’ fashion. This new approach, long-awaited and much-debated, promises to quickly lead to advances not just in the understanding of basic biological processes, but in the prevention, diagnosis and treatment of many genetic and genomic disorders. While the fruits of sequencing the human genome may not be known or appreciated for another hundred years, the implications to the basic way in which medicine will be practised in the future is staggering.

At the time of writing of this paper, the International Human Genome Sequencing Consortium had fully finished 24.7% of the human sequence, with another 66.2% of the sequence being available in draft form. In the course of this sequencing, two of the human chromosomes have been finished, namely chromosomes 21 and 22 (2,3). Even with most of the chromosomes incomplete, some interesting insights have already been made into the structure of the human genome, such as a decided down-estimate in the number of genes actually in the human genome. While most of the attention of the scientific community and the public at large has focused on the human sequence, a number of model organisms have also been sequenced, including that of the fruit fly (Drosophila melanogaster) in 2000 (4); the complete genomes of organisms such as the rat and the mouse will quickly follow over the next several years. Efforts are also focused on sequence variation, with the SNP Consortium anticipating the identification of a million single nucleotide polymorphisms (SNPs) by the end of 2000, far ahead of the initial goal of discovering 100 000 SNPs by 2003 (1).

Database efforts have kept pace with the furious rate at which this sequence data is being generated, providing investigators access to all public data in a practically instantaneous fashion (5). While most biologists are familiar with the databases comprising the International Nucleotide Sequence Database Collaboration (DDBJ, EMBL and GenBank), numerous other specialized databases have emerged. These specialized databases often arise out of a particular need, whether it be to address a particular biological question of interest or to better serve a particular segment of the biological community. This journal has devoted its first issue over the last several years to documenting the availability and features of these specialized databases in order to better serve its readership and to promote the use of these resources in the design and analysis of experiments. These reviewed databases are collectively listed in the Molecular Biology Database Collection.

The databases included in the current version of the Collection are shown in Table 1. This year, 55 new entries have been added, bringing the total number of databases listed to 281. While this number may seem large for a ‘curated collection’, these databases distinguish themselves by their approach to presenting the underlying data–for example, by adding new value to the underlying data by virtue of curation, by providing new types of data connections or by implementing other innovative approaches facilitating biological discovery. The individual entries are classified by type, but the reader should recognize that the distinctions between these classes are often arbitrary, and that many of these databases provide more than one type of information to the user.

Table 1. Molecular Biology Database Collection.

Major Sequence Repositories
DNA Data Bank of Japan (DDBJ)	http://www.ddbj.nig.ac.jp	All known nucleotide and protein sequences; International Nucleotide Sequence Database Collaboration
EMBL Nucleotide Sequence Database	http://www.ebi.ac.uk/embl.html	All known nucleotide and protein sequences; International Nucleotide Sequence Database Collaboration
GenBank	http://www.ncbi.nlm.nih.gov/	All known nucleotide and protein sequences; International Nucleotide Sequence Database Collaboration
Genome Sequence Database (GSDB)	http://www.ncgr.org/research/sequence/	All known nucleotide and protein sequences
STACK	http://www.sanbi.ac.za/Dbases.html	Non-redundant, gene-oriented clusters
TIGR Gene Indices	http://www.tigr.org/tdb/index.html	Non-redundant, gene-oriented clusters
UniGene	http://www.ncbi.nlm.nih.gov/UniGene/	Non-redundant, gene-oriented clusters
Comparative Genomics
Clusters of Orthologous Groups (COG)	http://www.ncbi.nlm.nih.gov/COG/	Phylogenetic classification of proteins from 21 complete genomes
XREFdb	http://www.ncbi.nlm.nih.gov/XREFdb/	Cross-referencing of model organism genetics with mammalian phenotypes
Gene Expression
ASDB	http://cbcg.nersc.gov/asdb	Protein products and expression patterns of alternatively-spliced genes
Axeldb	http://www.dkfz-heidelberg.de/abt0135/axeldb.htm	Gene expression in Xenopus
BodyMap	http://bodymap.ims.u-tokyo.ac.jp/	Human and mouse gene expression data
EpoDB	http://www.cbil.upenn.edu/epodb/	Genes expressed in vertebrate RBC
FlyView	http://pbio07.uni-muenster.de/	Drosophila development and genetics
Gene Expression Database (GXD)	http://www.informatics.jax.org/searches/gxdindex_form.shtml	Mouse gene expression and genomics
Interferon Stimulated Gene Database	http://www.lerner.ccf.org/labs/williams/xchip-html.cgi	Genes induced by treatment with interferons
Kidney Development Database	http://www.ana.ed.ac.uk/anatomy/database/kidbase/kidhome.html	Kidney development and gene expression
MAGEST	http://star.scl.kyoto-u.ac.jp/magest/	Ascidian (Halocynthia roretzi) gene expression patterns
MethDB	http://www.methdb.de	DNA methylation data, patterns and profiles
Mouse Atlas and Gene Expression Database	http://genex.hgu.mrc.ac.uk	Spatially-mapped gene expression data
PEDB	http://chroma.mbt.washington.edu/PEDB/	Normal and aberrant prostate gene expression
RECODE	http://recode.genetics.utah.edu	Genes using programmed translational recoding in their expression
Stanford Microarray Database	http://genome-www.stanford.edu/microarray	Raw and normalized data from microarray experiments
TRIPLES	http://ygac.med.yale.edu/triples/triples.htm	TRansposon-Insertion Phenotypes, Localization, and Expression in Saccharomyces
Tooth Development Database	http://bite-it.helsinki.fi/	Gene expression in dental tissue
Gene Identification and Structure
AllGenes	http://www.allgenes.org	Human and mouse gene index integrating gene, transcript and protein annotation
Ares Lab Intron Site	http://www.cse.ucsc.edu/research/compbio/yeast_introns.html	Yeast spliceosomal introns
AsMamDB	http://166.111.30.65/ASMAMDB.html	Alternatively-spliced mammalian genes
COMPEL	http://compel.bionet.nsc.ru/	Composite regulatory elements
CUTG	http://www.kazusa.or.jp/codon/	Codon usage tables
DBTBS	http://elmo.ims.u-tokyo.ac.jp/dbtbs/	Bacillus subtilis binding factors and promoters
EID	http://mcb.harvard.edu/gilbert/EID/	Protein-coding, intron-containing genes
EPD	http://www.epd.isb-sib.ch/	Eukaryotic POL II promoters with experimentally-determined transcription start sites
ExInt	http://intron.bic.nus.edu.sg/exint/exint.html	Exon-intron structure of eukaryotic genes
HUNT	http://www.hri.co.jp/HUNT	Annotated human full-length cDNA sequences
IDB/IEDB	http://nutmeg.bio.indiana.edu/intron/index.html	Intron sequence and evolution
PLACE	http://www.dna.affrc.go.jp/htdocs/PLACE	Plant cis-acting regulatory elements
PlantCARE	http://sphinx.rug.ac.be:8080/PlantCARE/index.htm	Plant cis-acting regulatory elements
PromEC	http://bioinfo.md.huji.ac.il/marg/promec	Escherichia coli mRNA promoters with experimentally identified transcriptional start sites
RRNDB	http://rrndb.cme.msu.edu	Variation in prokaryotic ribosomal RNA operons
STRBase	http://www.cstl.nist.gov/div831/strbase/	Short tandem DNA repeats
SpliceDB	http://genomic.sanger.ac.uk/spldb/SpliceDB.html	Canonical and non-canonical mammalian splice sites
TRRD	http://wwwmgs.bionet.nsc.ru/mgs/dbases/trrd4	Transcription regulatory regions of eukaryotic genes
TransTerm	http://uther.otago.ac.nz/Transterm.html	Codon usage, start and stop signals
VIDA	http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html	Virus genome open reading frames
WormBase	http://www.wormbase.org	Guide to Caernorhabditis elegans biology
YIDB	http://www.EMBL-Heidelberg.DE/ExternalInfo/seraphin/yidb.html	Yeast nuclear and mitochondrial intron sequences
rSNP Guide	http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/	Single nucleotide polymorphisms in regulatory gene regions
Genetic and Physical Maps
DRESH	http://www.tigem.it/LOCAL/drosophila/dros.html	Human cDNA clones homologous to Drosophila mutant genes
G3-RH	http://www-shgc.stanford.edu/RH/	Stanford G3 and TNG radiation hybrid maps
GB4-RH	http://www.sanger.ac.uk/Software/RHserver//Rhserver.shtml	Genebridge4 (GB4) human radiation hybrid maps
GDB	http://www.gdb.org	Human genes and genomic maps
GenAtlas	http://www.citi2.fr/GENATLAS/	Human genes, markers and phenotypes
GenMapDB	http://genomics.med.upenn.edu/genmapdb	Mapped human BAC clones
GeneMap ‘99	http://www.ncbi.nlm.nih.gov/genemap/	International Radiation Mapping Consortium human gene map
HuGeMap	http://www.infobiogen.fr/services/Hugemap	Human genome genetic and physical map data
IXDB	http://ixdb.mpimg-berlin-dahlem.mpg.de	Physical maps of human chromosome X
RHdb	http://www.ebi.ac.uk/RHdb	Radiation hybrid map data
Radiation Hybrid Database	http://www.ebi.ac.uk/RHdb	Radiation hybrid map data
Genomic Databases
ACeDB	http://www.sanger.ac.uk/Software/Acedb/	C.elegans, Saccharomyces pombe, and human sequences and genomic information
AMmtDB	http://bio-www.ba.cnr.it:8000/BioWWW/#AMMTDB	Metazoan mitochondrial DNA sequences
ArkDB	http://www.thearkdb.org/genome_mapping.html	Genome databases for farm and other animals
Comprehensive Microbial Resource	http://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl	Completed microbial genomes
CropNet	http://ukcrop.net/	Genome mapping in crop plants
CyanoBase	http://www.kazusa.or.jp/cyano/	Synechocystis sp. genome
EMGlib	http://pbil.univ-lyon1.fr/emglib/emglib.html	Completely sequenced microbial genomes from bacteria, archaea, yeast
EcoGene	http://bmb.med.miami.edu/EcoGene/EcoWeb/	E.coli K-12 sequences
FlyBase	http://www.fruitfly.org	Drosophila sequences and genomic information
Full-Malaria	http://133.11.149.55	Full-length cDNA library from erythrocytic-stage Plasmodium falciparum
GOBASE	http://megasun.bch.umontreal.ca/gobase/gobase.html	Organelle genome database
GOLD	http://igweb.integratedgenomics.com/GOLD/	Information regarding complete and ongoing genome projects
HIV Sequence Database	http://hiv-web.lanl.gov/	HIV RNA sequences
Human BAC Ends Database	http://www.tigr.org/tdb/humgen/bac_end_search/bac_end_intro.html	Non-redundant human BAC end sequences
ICB	http://www.mbio.co.jp/icb	Identification and classification of bacteria using protein-coding
INE	http://rgp.dna.affrc.go.jp/giot/INE.html	Rice genetic and physical maps and sequence data
MITOMAP	http://www.gen.emory.edu/mitomap.html	Human mitochondrial genome
MITOP	http://websvr.mips.biochem.mpg.de/proj/medgen/mitop	Mitochondrial proteins, genes, and diseases
Medicago Genome Initiative	http://www.noble.org/medicago/	Model legume Medicago truncatula ESTs, gene expression and proteomic data
Mendel Database	http://jiio6.jic.bbsrc.ac.uk/	Database of plant EST and STS sequences annotated with gene family information
MitBASE	http://www3.ebi.ac.uk/Research/Mitbase/mitbase.pl	Mitochondrial genomes, intra-species variants, and mutants
MitoDat	http://www-lecb.ncifcrf.gov/mitoDat/	Mitochondrial proteins (predominantly human)
MitoNuc/MitoAln	http://bio-www.ba.cnr.it:8000/srs6/	Nuclear genes coding for mitochondrial proteins
Mouse Genome Database (MGD)	http://www.informatics.jax.org	Mouse genetics and genomics
Munich Information Center for Protein Sequences (MIPS)	http://www.mips.biochem.mpg.de/	Protein and genomic sequences
NRSub	http://pbil.univ-lyon1.fr/nrsub/nrsub.html	B.subtilis genome
PlasmoDB	http://PlasmoDB.org	Plasmodium GENOME
RsGDB	http://www-mmg.med.uth.tmc.edu/sphaeroides	Rhodobacter sphaeroides genome
Saccharomyces Genome Database (SGD)	http://genome-www.stanford.edu/Saccharomyces	S.cerevisiae genome
TIGR Microbial Database	http://www.tigr.org/tdb/mdb/mdbcomplete.html	Microbual genomes and chromosomes
The Arabidopsis Information Resource (TAIR)	http://www.arabidopsis.org/	Arabidopsis thaliana genome
ZFIN	http://www.zfin.org	Genetic, genomic and developmental data from zebrafish
ZmDB	http://zmdb.iastate.edu/	Maize genome database
Intermolecular Interactions
Biomolecular Interaction Network Database (BIND)	http://binddb.org	Molecular interactions, complexes and pathways
DIP	http://dip.doe-mbi.ucla.edu/	Catalog of protein–protein interactions
DPInteract	http://arep.med.harvard.edu/dpinteract/	Binding sites for E.coli DNA-binding proteins
Database of Ribosomal Crosslinks (DRC)	http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc/	Ribosomal crosslinking data
Metabolic Pathways and Cellular Regulation
ENZYME	http://www.expasy.ch/enzyme/	Enzyme nomenclature
EcoCyc	http://ecocyc.pangeasystems.com/ecocyc/	E.coli K-12 genome, gene products, and metabolic pathways
EpoDB	http://www.cbil.upenn.edu/EpoDB/	Genes expressed during human erythropoiesis
FlyNets	http://gifts.univ-mrs.fr/FlyNets/FlyNets_home_page.html	Drosophila melanogaster molecular interactions
Klotho	http://www.ibc.wustl.edu/klotho/	Collection and categorization of biological compounds
Kyoto Encyclopedia of Genes and Genomes (KEGG)	http://www.genome.ad.jp/kegg	Metabolic and regulatory pathways
LIGAND	http://www.genome.ad.jp/dbget/ligand.html	Enzymatic ligands, substrates and reactions
RegulonDB	http://www.cifn.unam.mx/Computational_Biology/regulondb/	E.coli transcriptional regulation and operon organization
UM-BBD	http://www.labmed.umn.edu/umbbd/	Microbial biocatalytic reactions and biodegradation pathways
WIT2	http://wit.mcs.anl.gov/WIT2/	Integrated system for functional curation and development of metabolic models
Mutation Databases
16S and 23S Ribosomal RNA Mutation Databases	http://ribosome.fandm.edu	16S and 23S ribosomal RNA mutation database
ALFRED	http://alfred.med.yale.edu/alfred/index.asp	Allele frequencies and DNA polymorphisms
Androgen Receptor Gene Mutations Database	http://www.mcgill.ca/androgendb/	Mutations in the androgen receptor gene
Asthma Gene Database	http://cooke.gsf.de/asthmagen/main.cfm	Linkage and mutation studies on the genetics of asthma and allergy
Asthma and Allergy Database	http://cooke.gsf.de/asthmagen/main.cfm
Atlas of Genetics and Cytogenetics in Oncology and Haematology	http://www.infobiogen.fr/services/chromcancer/	Chromosomal abnormalities in cancer
BTKbase	http://www.uta.fi/laitokset/imt/bioinfo/BTKbase/	Mutation registry for X-linked agammaglobulinemia
CASRDB	http://data.mch.mcgill.ca/casrdb/	CASR mutations causing FHH, NSHPT and ADH
Cytokine Gene Polymorphism Database	http://www.pam.bris.ac.uk/services/GAI/cytokine4.htm	Cytokine gene polymorphisms, in vitro expression and disease-association studies
Database of Germline p53 Mutations	http://www.lf2.cuni.cz/win/projects/germline_mut_p53.htm	Mutations in human tumor and cell line p53 gene
GRAP Mutant Databases	http://tinyGRAP.uit.no/GRAP/	Mutants of family A G-Protein Coupled Receptors (GRAP)
HGBASE	http://hgbase.cgr.ki.se	Intragenic sequence polymorphisms
HIV-RT	http://hivdb.stanford.edu/hiv/	HIV reverse transcriptase and protease sequence variation
Haemophila B Mutation Database	http://www.umds.ac.uk/molgen/haemBdatabase.htm	Point mutations, short additions and deletions in the Factor IX gene
Human Gene Mutation Database (HGMD)	http://www.uwcm.ac.uk/uwcm/mg/hgmd0.html	Known (published) gene lesions underlying human inherited disease
Human PAX2 Allelic Variant Database	http://www.hgu.mrc.ac.uk/Softdata/PAX2/	Mutations in human PAX2 gene
Human PAX6 Allelic Variant Database	http://www.hgu.mrc.ac.uk/Softdata/PAX6/	Mutations in human PAX6 gene
Human Type I and Type III Collagen Mutation Database	http://www.le.ac.uk/genetics/collagen/	Human type I and type III collagen gene mutations
HvrBase	http://db.eva.mpg.de/Hvrbase/	Primate mtDNA control region sequences
KMDB	http://mutview.dmb.med.keio.ac.jp/mutview3/kmeyedb/index.html	Mutations in human eye disease genes
KinMutBase	http://www.uta.fi/imt/bioinfo/KinMutBase/	Disease-causing protein kinase mutations
MmtDB	http://www.ba.cnr.it/∼areamt08/MmtDBWWW.htm	Mutations and polymorphisms in metazoan mitochondrial DNA sequences
Mutation Spectra Database	http://info.med.yale.edu/mutbase/	Mutations in viral, bacterial, yeast and mammalian genes
NCL Mutations	http://www.ucl.ac.uk/ncl/	Mutations and polymorphisms in neuronal ceroid lipofuscinoses (NCL) genes
Online Mendelian Inheritance in Man	http://www.ncbi.nlm.nih.gov/Omim/	Catalog of human genetic and genomic disorders
PAHdb	http://www.mcgill.ca/pahdb/	Mutations at the phenylalanine hydroxylase locus
PHEXdb	http://data.mch.mcgill.ca/phexdb	Mutations in PHEX gene causing X-linked hypophosphatemia
PMD	http://pmd.ddbj.nig.ac.jp/	Compilation of protein mutant data
PTCH1 Mutation Database	http://www.cybergene.se/PTCH/ptchbase.html	Mutations and SNPs found in PTCH1
RB1 Gene Mutation Database	http://www.d-lohmann.de/Rb/	Mutations in the human retinoblastoma (RB1) gene
Ribosomal RNA Mutational Database	http://ribosome.fandm.edu/	16S and 23S ribosomal RNA mutation database
SV40 Large T-Antigen Mutant Database	http://bigdaddy.bio.pitt.edu/SV40/	Mutations in SV40 large tumor antigen gene
dbSNP	http://www.ncbi.nlm.nih.gov/SNP/	Single nucleotide polymorphisms
iARC p53 Database	http://www.iarc.fr/p53/	Missense mutations and small deletions in human p53 reported in peer-reviewed literature
p53 Databases	http://metalab.unc.edu/dnam/mainpage.html	Mutations at the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations
Pathology
FIMM	http://sdmc.krdl.org.sg:8080/fimm/	Functional molecular immunology data
HCForum	http://hcforum.imag.fr/welcome_eng.html	Human cytogenetics database
Mouse Tumor Biology Database (MTB)	http://tumor.informatics.jax.org	Mouse tumor names, classification, incidence, pathology, genetic factors
Oral Cancer Gene Database	http://www.tumor-gene.org/Oral/oral.html	Cellular, molecular and biological data for genes involved in oral cancer
PEDB	http://chroma.mbt.washington.edu/PEDB/	Sequences from prostate tissue and cell type-specific cDNA libraries
Tumor Gene Family Databases (TGDBs)	http://www.tumor-gene.org/tgdf.html	Cellular, molecular, and biological data about genes involved in various cancers
Protein Databases
AARSDB	http://rose.man.poznan.pl/aars/index.html	Aminoacyl-tRNA synthetase sequences
ABCdb	http://ir2lcb.cnrs-mrs.fr/ABCdb/	ABC transporters
DAtA	http://luggagefast.Stanford.EDU/group/arabprotein/	Annotated coding sequences from Arabidopsis
DExH/D Family Database	http://www.columbia.edu/~ej67/dbhome.htm	DEAD-box, DEAH-box and DExH-box proteins
ESTHER	http://www.ensam.inra.fr/cholinesterase/	Esterases and alpha/beta hydrolase enzymes and relatives
Endogenous GPCR List	http://www.biomedcomp.com/GPCR.html	G protein-coupled receptors; expression in cell lines
FUNPEP	http://www.gpcr.org/FUNPEP/db	Low-complexity or compositionally-biased protein sequences
GPCRDB	http://swift.embl-heidelberg.de/7tm/	G protein-coupled receptors
GenProtEC	http://genprotec.mbl.edu	Escherichia coli K-12 genome, gene products and homologs
HIV Molecular Immunology Database	http://hiv-web.lanl.gov/immunology/	HIV epitopes
HUGE	http://www.kazusa.or.jp/huge/	Large (50 kDa) human proteins and cDNA sequences
Histone Database	http://genome.nhgri.nih.gov/histones/	Histone and histone fold sequences and structures
Homeobox Page	http://copan.bioz.unibas.ch/homeo.html	Information relevant to homeobox proteins, classification and evolution
Homeodomain Resource	http://genome.nhgri.nih.gov/homeodomain	Homeodomain sequences, structures, and related genetic and genomic information
IMGT	http://imgt.cines.fr:8104/	Immunoglobulin, T cell receptor and MHC sequences from human and other vertebrates
IMGT/HLA	http://www.ebi.ac.uk/imgt/hla/	Human major histocompatibility complexes
InBase	http://www.neb.com/neb/inteins.html	Intervening protein sequences (inteins) and motifs
Kabat Database	http://immuno.bme.nwu.edu/	Sequences of proteins of immunological interest
LGICdb	http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html	Ligand-gated ion channel subunit sequences
MEROPS	http://www.merops.co.uk	Proteolytic enzymes (proteases/peptidases)
MHCPEP	http://wehih.wehi.edu.au/mhcpep/	MHC-binding peptides
Membrane Protein Database	http://biophys.bio.tuat.ac.jp/ohshima/database/	Membrane protein sequences, transmembrane regions and structures
MetaFam	http://metafam.ahc.umn.edu/	Integrated protein family information
Nuclear Receptor Resource	http://nrr.georgetown.edu/nrr/nrr.html	Nuclear receptor superfamily
Olfactory Receptor Database	http://ycmi.med.yale.edu/senselab/ordb/	Sequences for olfactory receptor-like molecules
PKR	http://pkr.sdsc.edu	Protein kinase sequences, enzymology, genetics, and molecular and structural properties
PPMdb	http://sphinx.rug.ac.be:8080/ppmdb/index.html	Arabidopsis plasma membrane protein sequence and expression data
PROMISE	http://bioinf.leeds.ac.uk/promise/	Prosthetic centers and metal ions in protein active sites
Peptaibol	http://www.cryst.bbk.ac.uk/peptaibol/welcome.html	Peptaibol (antibiotic peptide) sequences
PhosphoBase	http://www.cbs.dtu.dk/databases/PhosphoBase/	Protein phosphorylation sites
PlantsP	http://PlantsP.sdsc.edu	Plant protein kinases and protein phosphatases
Prolysis	http://delphi.phys.univ-tours.fr/Prolysis/	Proteases and natural and synthetic protease inhibitors
Protein Information Resource (PIR)	http://pir.georgetown.edu	Comprehensive, annotated, non-redundant protein sequence database
Ribonuclease P Database	http://www.mbio.ncsu.edu/RNaseP/home.html	RNase P sequences, alignments and structures
SENTRA	http://wit.mcs.anl.gov/WIT2/Sentra/HTML/sentra.html	Sensory signal transduction proteins
SWISS-PROT/TrEMBL	http://www.expasy.ch/sprot	Curated protein sequences
TIGRFAMs	http://www.tigr.org/TIGRFAMs	Protein family resource for the functional identification of proteins
TRANSFAC	http://transfac.gbf.de/TRANSFAC/index.html	Transcription factors and binding sites
Wnt Database	http://www.stanford.edu/~rnusse/wntwindow.html	Wnt proteins and phenotypes
ooTFD	http://www.ifti.org/	Transcription factors and gene expression
trEST, trGEN and Hits	http://hits.isb-sib.ch	Predicted protein sequences
Protein Sequence Motifs
BLOCKS	http://blocks.fhcrc.org/	Conserved sequence regions of protein families
CluSTr	http://www.ebi.ac.uk/clustr/	Automatic classification of SWISS-PROT+TrEMBL proteins into related groups
InterPro	http://www.ebi.ac.uk/interpro/	Integrated documentation resource for protein families, domains and sites
O-GLYCBASE	http://www.cbs.dtu.dk/databases/OGLYCBASE/	Glycoproteins and O-linked glycosylation sites
PIR-ALN	http://www-nbrf.georgetown.edu/pirwww/dbinfo/piraln.html	Protein sequence alignments
PRINTS	http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/	Hierarchical gene family fingerprints
PROSITE	http://www.expasy.ch/prosite/	Biologically-significant protein patterns and profiles
Pfam	http://www.sanger.ac.uk/Software/Pfam/	Multiple sequence alignments and hidden Markov models of common protein domains
ProClass	http://pir.georgeown.edu/gfserver/proclass.html	Protein families defined by PIR superfamilies and PROSITE patterns
ProDom	http://www.toulouse.inra.fr/prodom.html	Protein domain families
ProtoMap	http://www.protomap.cs.huji.ac.il/	Automated hierarchical classification of SWISS- PROT proteins
SBASE	http://www3.icgeb.trieste.it/~sbasesrv/	Annotated protein domain sequences
SMART	http://smart.embl-heidelberg.de/	Signaling domain sequences
SYSTERS	http://www.dkfz-heidelberg.de/tbi/services/cluster/systersform	Classification of protein sequences into disjoint clusters with annotations from various other resources
eMOTIF	http://motif.stanford.edu/emotif	Protein sequence motif determination and searches
iPROCLASS	http://pir.georgetown.edu/iproclass/	Annotated protein classification database
Proteome Resources
AAindex	http://www.genome.ad.jp/dbget/	Physicochemical properties of peptides
Proteome Analysis Database	http://www.ebi.ac.uk/proteome/	Online application of interpro and clustr for the functional classification of proteins in whole genomes
REBASE	http://rebase.neb.com/rebase/rebase.html	Restriction enzymes and associated methylases
SWISS-2DPAGE	http://www.expasy.ch/ch2d/	Annotated two-dimensional polyacrylamide gel electrophoresis database
Yeast Proteome Database (YPD)	http://www.proteome.com/databases/index.html	S.cerevisiae proteome
RNA Sequences
5S Ribosomal RNA Database	http://biobases.ibch.poznan.pl/5SData/	5S rRNA sequences
ACTIVITY	http://wwwmgs.bionet.nsc.ru/mgs/systems/activity/	Functional DNA/RNA site activity
ARED	http://rc.kfshrc.edu.sa	AU-rich element-containing mRNAs
Collection of mRNA-like Noncoding RNAs	http://biobases.ibch.poznan.pl/ncRNA/	Non-protein-coding RNA transcripts
European Large Subunit Ribosomal RNA Database	http://rrna.uia.ac.be/lsu/index.html	Alignment of large subunit ribosomal RNA sequences with secondary structure information
European Small Subunit Ribosomal RNA Database	http://rrna.uia.ac.be/ssu/index.html	Alignment of small subunit ribosomal RNA sequences with secondary structure information
Guide RNA Database	http://www.biochem.mpg.de/~goeringe/	Guide RNA sequences
HyPaLib	http://bibiserv.techfak.uni-bielefeld.de/HyPa/	Structural elements characteristic for classes of RNA
Intronerator	http://www.cse.ucsc.edu/~kent/intronerator/	RNA splicing and gene structure in C.elegans; alignments of Caernorhabditis briggsae and C.elegans genomic sequences
Non-Canonical Interactions in RNA	http://prion.bchs.uh.edu/bp_type/	Non-standard base-base interactions in known RNA structures
PLMItRNA	http://bigarea.area.ba.cnr.it:8000/PLMItRNA/	Mitochondrial tRNA genes and molecules in photosynthetic eukaryotes
Pseudobase	http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html	Information on RNA pseudoknots
RISCC	http://ulises.umh.es/RISSC	Ribosomal 16S-23S RNA gene spacer regions
RNA Modification Database	http://medlib.med.utah.edu/RNAmods/	Naturally modified nucleosides in RNA
Ribosomal Database Project (RDP)	http://rdp.cme.msu.edu/	rRNA sequences, alignments and phylogenies
SELEXdb	http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/	Selected DNA/RNA functional site sequences
SRPDB	http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html	Signal recognition particle RNA, protein and receptor sequences
Small RNA Database	http://mbcr.bcm.tmc.edu/smallRNA	Direct sequencing of small RNA sequences from prokaryotes and eukaryotes
The tmRNA Website	http://www.indiana.edu/~tmrna	tmRNA sequences, foldings and alignments
UTRdb/UTRsite	http://bigarea.area.ba.cnr.it:8000/EmbIT/UTRHome/	5′’ and 3′’ UTRs of eukaryotic mRNAs and relevant functional patterns
Viroids and viroid-like RNAs	http://nt.ars-grin.gov/subviral/	Viroids and viroid-like RNAs
Yeast snoRNA Database	http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html	Yeast small nucleolar RNA
tRNA Sequences	http://www.uni-bayreuth.de/departments/biochemie/trna/	TRNA and tRNA gene sequences
tmRDB	http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html	TmRNA (10Sa RNA) sequences
Retrieval Systems and Database Structure
KEYnet	http://www.ba.cnr.it/keynet.html	Hierarchical list of gene and protein names for data retrieval
TESS	http://www.cbil.upenn.edu/tess	Transcription element search system
Virgil	http://www.infobiogen.fr/services/virgil	Database interconnectivity
Structure
ASTRAL	http://astral.stanford.edu/	Sequences of domains of known structure, selected subsets and sequence-structure correspondences
BioImage	http://www-embl.bioimage.org/	Searchable database of multidimensional biological images
BioMagResBank	http://www.bmrb.wisc.edu/	NMR spectroscopic data from proteins, peptides and nucleic acids
CATH	http://www.biochem.ucl.ac.uk/bsm/cath/	Hierarchical classification of protein domain structures
CE	http://cl.sdsc.edu/ce.html	CE: A Resource to Compute and Review 3-D Protein Structure Alignments
CKAAPs DB	http://cl.sdsc.edu/ckaap	Structurally-similar proteins with dissimilar sequences
CSD	http://www.ccdc.cam.ac.uk/prods/csd/csd.html	Crystal structure information for organic and metal organic compounds
Database of Macromolecular Movements	http://bioinfo.mbb.yale.edu/MolMovDB/	Descriptions of protein and macromolecular motions, including movies
Decoys ‘R’ Us	http://dd.stanford.edu/	Computer-generated protein conformations based on sequence data
HIC-Up	http://alpha2.bmc.uu.se/hicup/	Structures of small molecules (hetero-compounds)
HSSP	http://www.sander.ebi.ac.uk/hssp/	Structural families and alignments; structurally-conserved regions and domain architecture
IMB Jena Image Library of Biological Macromolecules	http://www.imb-jena.de/IMAGE.html	Visualization and analysis of three-dimensional biopolymer structures
ISSD	http://www.protein.bio.msu.su/issd/	Integrated sequence and structural information
LPFC	http://www-smi.stanford.edu/projects/helix/LPFC/	Library of protein family core structures
MMDB	http://www.ncbi.nlm.nih.gov/Structure/	All experimentally-determined three-dimensional structures, linked to NCBI Entrez
ModBase	http://pipe.rockefeller.edu/modbase	Annotated comparative protein structure models
NDB	http://ndbserver.rutgers.edu/NDB/ndb.html	Nucleic acid-containing structures
NTDB	http://ntdb.chem.cuhk.edu.hk	Thermodynamic data for nucleic acids
PALI	http://pauling.mbu.iisc.ernet.in/~pali	Phylogeny and alignment of homologous protein structures
PDB	http://www.rcsb.org/pdb/	Structure data determined by X-ray crystallography and NMR
PDB-REPRDB	http://www.rwcp.or.jp/papia/	Representative protein chains, based on PDB entries
PDBsum	http://www.biochem.ucl.ac.uk/bsm/pdbsum	Summaries and analyses of PDB structures
PRESAGE	http://presage.berkeley.edu/	Protein structures with experimental and predictive annotations
ProTherm	http://www.rtc.riken.go.jp/jouhou/protherm/protherm.html	Thermodynamic data for wild-type and mutant proteins
RESID	http://www-nbrf.georgetown.edu/pirwww/dbinfo/resid.html	Protein structure modifications
SCOP	http://scop.mrc-lmb.cam.ac.uk/scop/	Familial and structural protein relationships
SLoop	http://www-cryst.bioc.cam.ac.uk/~sloop/	Classification of protein loops
Transgenics
Cre Transgenic Database	http://www.mshri.on.ca/nagy/cre.htm	Cre transgenic mouse lines
Transgenic/Targeted Mutation Database	http://tbase.jax.org/	Information on transgenic animals and targeted mutations
Varied Biomedical Content
BAliBASE	http://www-igbmc.u-strasbg.fr/BioInfo/BaliBASE2/index.html	Benchmark database for comparison of multiple sequence alignments
DBcat	http://www.infobiogen.fr/services/dbcat/	Catalog of databases
DrugDB	http://pharminfo.com/drugdb/db_mnu.html	Pharmacologically-active compounds; generic and trade names
END	http://www.ibc.wustl.edu/biognosis/agora_interface/html/agora_entrance.html	Enzyme nomenclature
Global Image Database	http://www.gwer.ch/qv/gid/gid.htm	Annotated biological images
GlycoSuiteDB	http://www.glycosuite.com	N- and O-linked glycan structures and biological source information
HOX-PRO	http://www.mssm.edu/molbio/hoxpro/new/hox-pro00.html	Clustering of homeobox genes
Imprinted Genes and Parent-of-Origin Effects	http://www.otago.ac.nz/IGC	Imprinted genes and parent-of-origin effects in animals
LocusLink/RefSeq	http://www.ncbi.nlm.nih.gov/LocusLink/	Curated sequence and descriptive information about genetic loci
MPDB	http://www.biotech.ist.unige.it/interlab/mpdb.html	Information on synthetic oligonucleotides proven useful as primers or probes
Molecular Probe Database	http://srs.ebi.ac.uk/	Synthetic oligonucleotides, probes and PCR primers
NCBI Taxonomy Browser	http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html	Names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence
PubMed	http://www.ncbi.nlm.nih.gov/PubMed/	MEDLINE and Pre-MEDLINE citations
Tree of Life	http://phylogeny.arizona.edu/tree/phylogeny.html	Information on phylogeny and biodiversity
Vectordb	http://vectordb.atcg.com/	Characterization and classification of nucleic acid vectors

In addition to the list presented in this paper, an electronic version of the Database Issue and Collection can be accessed online and is freely available to everyone, regardless of subscription status, at http://www.nar.oupjournals.org. While the list contains the databases described in the papers comprising the current issue, it should be immediately apparent to the reader that there are simply not enough pages in this journal to accommodate full-length, printed descriptions of all 281 of the databases featured here. To address this, the online version of the Collection now includes short summaries of many of the databases, the summaries having been provided directly by the investigators responsible for the individual databases. It is hoped that this approach will provide the reader with an additional source of information that will facilitate finding and selecting the sources of data that would be of most value in addressing a specific biological problem. Contributors will be encouraged to keep their entries up-to-date, as the online descriptions will be updated on a regular basis.

Suggestions for the inclusion of additional database resources in this Collection are encouraged and may be directed to the author (andy@nhgri.nih.gov).