General
   Main page   
   FTP site   

Software
   CPDL   

Research Projects
   FACE   
   SP-GSTs   
   SACO   
   GSTs   
   NHEJ SNPs   
   Vector Development   

Sequencing projects
   B. Burgdorferi   
   R. Metallidurans   
   Clostridium BC1   

Around BNL
   Biology Dept.   
   BNL   
   BNL directory   

Biology Resources
   Genome Centers   
   Databases   
   Software   
   Miscellany   
   Links   
            
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

Protein

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

Organism-specific

Prokaryotes

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

Eukaryotes

Microorganims
Saccharomyces - Yeast genome (Stanford)
Plants
Arabidopsis thaliana
AtDB
Rice
Cornell, CSHL
Cotton
ACECOT - Cotton genome (BNL)
Maize
Genome: MaizeDB (U. Missouri, Columbia), ACEMAZ (BNL)
Animals
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 (mccorkle@bnl.gov).

DOE/BNL Privacy & Security Notice