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Biological Databases

[ Sequence | Protein | Prokaryote | Eurkaryotes ]

DNA Sequence

NCBI databases:
      NCBI FTP site - lots of data
      Genbank - sequence database
      UniGene - unique gene database
      Genomes - complete genomes (bacteria, archea, eukaryota, viruses, organelles)
      CGAP - Cancer Genome Anatomy Project
DDBJ - DNA Databank of Japan
EMBL databases
GDB - genome database
UTRdb - Untranslated Regions of Eukariotic mRNAS (Bari)
RDP - Ribosomal Database Project
rrndb - Ribosomal RNA Operon Copy Number Database
REBASE - restriction enzymes
DOGS - Database of Genome Sizes
miRBase - microRNA database


PDB - 3D structures (FTP)
SWISS-PROT - Annotated protein sequences
PROSITE - Protein families and domains
ProDom - Protein Domain Database
FSSP - Fold classification based on Structure-Structure alignment of Proteins
DALI - Dali Domain Dictionary
SYSTERS - Protein Family Database
Codon Usage Database - (Kazusa, Japan)
HGNC - HUGO Gene Nomenclature Committtee (UK)
HMM databases
Pfam - Protein families database of alignments and HMMs
TIGRFAMs - Protein families based on Hidden Markov Models or HMMs (TIGR)
Superfamily - HMM library and genome assignments at the protein superfamily level
SMART - Simple Modular Architecture Research Tool
SCOP - Structural Classification of Proteins



Borrelia burgdorferi - a l'Institut Pasteur
E. coli K-12 W3110 - Japan
HIDB - Haemophilus influenzae Rd genome (TIGR)
MGDB - Mycoplasma genitalium genome (TIGR)
NRSub - Non-redundant Bacillus subtilis
MycDB - Mycobacterium


Saccharomyces - Yeast genome (Stanford)
Arabidopsis thaliana
Cornell, CSHL
ACECOT - Cotton genome (BNL)
Genome: MaizeDB (U. Missouri, Columbia), ACEMAZ (BNL)
FlyBase - Drosophila Genome
Caenorhabditis elegans: UT SWM, CSHL
Mouse - Jackson
Homo sapiens - Human (see JGI Sanger, TIGR, UCSC, Wash U)

Last updated 11:43 pm, Jan 21, 2010
Maintained by Sean R. McCorkle (

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