Additional Molecular Biology Databases

Each year Nucleic Acids Research publishes a special issue describing a wide variety of databases containing useful compilations of sequence and other information. They was complied by Dr. Michael Galperin from NCBI in Bethesda. An abbreviated list of databases is shown below. The entire 2008 list of over 1000 databases is available as a searchable, up-to-date, online resource at: http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D2.

Database	URL	Description
Nucleotide Sequence
GenBank	www.ncbi.nlm.nih.gov	All publicly available nucleotide and protein sequences
EMBL Nucleotide Sequence Database	www.ebi.ac.uk/embl.html	All publicly available nucleotide and protein sequences
DNA Data Bank of Japan (DDBJ)	www.ddbj.nig.ac.jp	All publicly available nucleotide and protein sequences
DNA Sequences: Genes, Motifs and Regulatory Sites
TIGR Gene Indices	www.tigr.org/tdb/tgi.shtml	Organism-specific databases of EST and gene sequences
ExInt	sege.ntu.edu.sg/wester/iekb/	Exon-intron structure of eukaryotic genes
TRANSFAC	www.gene-regulation.com	Transcription factors and binding sites
RDP	rdp.cme.msu.edu	Ribosomal database project: rRNA sequences data
Gene Expression
PIR	pir.georgetown.edu	A collection of protein sequence databases
SWISS-PROT	www.expasy.ch/sprot	Curated protein sequence databases
PROSITE	www.expasy.ch/prosite	Biologically-significant protein patterns and profiles
Pfam	www.sanger.ac.uk/Software/Pfam/	Sequence alignments and profile hidden Markov models
Carbohydrate
CCSD	bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm	Complex carbohydrate structure databases (CarbBank)
Protein Structure
PDB	www.rcsb.org/pdb/	All available 3D structures of proteins and nucleic acids
Genomics
GO	www.geneontology.org	Gene onthology consortium database
KEGG	www.genome.ad.jp/kegg	Databases of genes, proteins, and metabolic pathways
EcoCyc	ecocyc.org	E. coli K-12 genes, metabolic pathways, transporters, regulation
Ensembl	www.ensembl.org	Annotated information on eukaryotic genomes