General
Main page
FTP site
Software
CPDL
Research
SP-GSTs
SACO
GSTs
SAGE
NHEJ SNPs
Vector Development
Sequencing
B. Burgdorferi
R. Metallidurans
Clostridium BC1
Around BNL
Biology Dept.
Proteome
ADSP
Plant Genomes
BNL
BNL directory
Biology Resources
Genome Centers
Databases
Organisms
Software
Educational
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
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)
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