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Sequence, Structure & Function Databases
Nucleic Acid Databases |Protein Databases |Carbohydrate Databases |Model Organisms Databases

DNA & RNA Databases
Major Sequence Repositories - Human Chromosome Information - Organelle Genome Databases - RNA Databases - Comparative & Phylogenetic Databases - SNPs,
 Mutations and Variations Databases - Alternative Splicing Databases - Specialized Databases 

Major Sequence Repositories:
DDBJ: DNA databank of Japan
EMBL: Maintained by EMBL
GenBank: Maintained by NCBI
Human Chromosome Information:
Click the link below to access chromosome information
1 2 3 4
5 6 7 8
9 10 11 12
13 14 15 16
17 18 19 20
21 22 X Y

Organelle Genome Databases:
OGMP:  Organell genome megasequencing program
GOBASE:  An organelle genome database
MitoMap:  Human mitochondrial genome database

RNA Databases:
Rfam: RNA familiy database
RNA base:   Database of RNA structures

tRNA database:   Database of  tRNAs
tRNA:  tRNA sequences and genes
sRNA:  Small RNA database

Comparative & Phylogenetic Databases:
COG:  Phylogenetic classification of proteins 
DHMHD:  Human-mouse homology database
HomoloGene:  Gene homologies across species
Homophila:  Human disease to Drosophila gene database
HOVERGEN:  Database of homologous vertebrate genes 
TreeBase:  A database of phylogenetic knowledge
XREF:  Cross-referencing with model organisms

SNPs, Mutations & Variations Databases:
ALPSbase: Database of mutations causing human ALPS
dbSNP:  Single nucleotide polymorphism database at NCBI
HGVbase:   Human Genome Variation database

Alternative Splicing Databases:
ASAP: Alternate splicing analysis tool at UCLA
ASG: Alternate splicing gallery
HASDB:  Human alternative splicing database at UCLA
AsMamDB:  alternatively spliced genes in human, mouse and rat
ASD: Alternative splicing database at CSHL
Specialised Databases:
ABIM:  Links to several genomics database
ACUTS:  Ancient conserved untranslated sequences
AGSD: Animal genome size database
AmiGO: The Gene Ontology database
ARGH: The acronym database
ASDB:  Database of alternatively spliced genes

BACPAC:  BAC and PAC genomic DNA library info
BBID: Biological Biochemical image database
Cardiac gene database:
CHLC:  Genetic markers on chromosomes
COGENT: Complete genome tracking database
COMPEL: Composite regulatory elements in eukaryotes 
CUTG:  Codon usage database 
dbEST:  Database of expressed sequences or mRNA
dbGSS: Genome survey sequence database
dbSTS: Sequence tagged sites (STS)
DBTSS: Database of transcriptional start sites
DOGS:  Database of genome sizes
EID:  The exon-intron database - Harvard
Exon-Intron: Exon-Intron database - Singapore
EPD:  Eukaryotic promotor database
FlyTrap: HTML based gene expression database
GDB:  The genome database
GenLink:  Resources for human genetic and telomere research 
GeneKnockouts:  Gene knockout information
GENOTK:  Human cDNA database
GEO:  Gene expression omnibus NCBI
GOLD:  Information on genome projects around the world
GSDB:The Genome Sequence DataBase
HGI:  TIGR human gene index
HTGS: High-through-put genomic sequence at NCBI
IMAGE:  The largest collection of DNA sequences clones
IMGT:   The international ImMunoGeneTics information system
IPCN:  Index to Plant Chromosome Numbers database
LocusLink:  Single query interface to sequence and genetic loci
TelDB:  The telomere database
MitoDat: Mitochondrial nuclear genes
Mouse EST:   NIA mouse cDNA project
MPSS: Searchable databases of several species
NDB:  Nucleic acid database
NEDO:  Human cDNA sequence database
NPD: Nuclear protein database
Oomycetes DB: Oomycetes database at Virginia Bioinformatics Institute
PLACE: Database of plant cis-acting regulatory DNA elements
RDP:  Ribosomal database project
RDB:  Receptor database at NIHS, Japan
Refseq: The NCBI reference sequence project
RHdb: Radiation hybrid physical map of chromosomes
SHIGAN: SHared Information of GENetic resources, Japan
SpliceDB:  Canonical and non-canonical splice site sequences
STACK:  Consensus human EST database
TAED:  The adaptive evolution database
TIGR:  Curated databases of microbes, plants and humans
TRANSFAC: The Transcription Factor Database
TRRD:  Transcription Regulatory region database
UniGene: Cluster of sequences for unique genes at NCBI
UniSTS:  Nonredundent collection of STS  

Protein Databases
Protein Sequence Databases - Protein Structure Databases - Protein Domains, Motifs and Signatures - Others
Protein Sequence Databases:
Antibodies: Sequence and Structure
BRENDA: Enzyme database
CD Antigens:  Database of CD antigens
dbCFC:  Cytokine family database
Histons:  Histone sequence database
HPRD:  Human protein reference database
InterPro: Intergrated documentation 5resources for protein families
iProClass: An integrated protein classification database
KIND:  A non-redundant protein sequence database
MHCPEP:  Database of MHC binding peptides
MIPS:  Munich information centre for protein sequences
PIR:  Annotated, and non-redundant protein sequence database
PIR-ALN: Curated database of protein sequence alignments
PIR-NREF: PIR nonredundent reference protein database
PMD:  Protein mutant database
PRF: Protein research foundation, Japan
ProClass: Non-redundant protein database
ProtoMap:  Hierarchical classification of swissprot proteins
REBASE:  Restriction enzyme database
RefSeq:   Reference sequence database at NCBI
SwissProt:  Curated protein sequence database
Comprehensive protein sequence database
Transfac:  Transcription factor database
TrEMBL:  Annotated translations of EMBL nucleotide sequences
Tumor gene database:  Genes with cancer-causing mutations
WD repeats:  WD-repeat family of proteins
Protein Structure Databases:
Cath:  Protein structure classification
HIV Protease:   HIV protease database 3D structure
PDB:  3-D macromolecular structure data
PSI: Protein structure initiative
S2F: Structure to function project
Scop:  Structural Classification of Proteins
Protein Domains, Motifs & Signatures:
BLOCKS:  Multipe aligned segments of conserved protein regions
CCD:  Conserved domain database and search service
DOMO:  Homologous protein domain families
Pfam:  Database of protein domains and HMMs
ProDom:  Protein domain database
Prints:  Protein motif fingerprint database
Prosite:   Database of protein families and domains
SMART:  Simple modular architecture research tool
TIGRFAM: Protein families based on HMMs

Phospho Site:   Database of phosphorylation sites
PROW:  Protein reviews on the web
Protein Lounge: Complete systems biology
Other Databases
Carbohydarate Databases

Carb DB: Carbohydrate Sequence and Structure Database
GlycoWord: Glycoscience related information
SPECARB: Raman Spectra of carbohydrates

Other Databases
AlzGene: Alzheimer’s disease
Polygenic pathways : Alzheimer's disease, Bipolar disorder or Schizophrenia

Model Organism Databases and Resources

Arabidopsis - Bacteria - Sea Bass - Cat - Cattle - Chicken - Cotton - CyanoBacteria - Daphnia - Deer - Dictyostelium - Dog - Frog - Fruit Fly - Fungus - Goat - Horse - Madaka Fish - Maize - Malaria - Mosquito - Mouse - Pig - Plants - Protozoa - Puffer Fish - Rat - Rice - Rickettsia - Salmon - Sheep - Soy - Sorgham - Tetradon - Tilapia - Turkey - Viruses - Worm - Yeast - Zebra Fish

General Information
GMOD: Generic Model Organism Database
Model Organisms:
 The WWW virtual library of model organisms

Arabidopsis thaliana
ABRC: Arabidopsis biological resource center
AGI: Arabidopsis genome initiative 
AREX: Arabidopsis gene expression database
Arabinet:  Arabidopsis information on the www
AtGDB: An Arabidopsis thalina plant genome database
AtGI: TIGR Arabidopsis thaliana gene index
ATGC:  Genome sequencing at ATGC
ATIDB: Arabidopsis insertion database
CSHL: Arabidopsis genome analysis at Cold Spring
ESSA: Arabidopsis thalina project at MIPS
Genoscope:  AGI in France
Kazusa:  Arabidopsis thaliana genome info Japan
MPSS: Massively parallel signature sequencing
NASC: Nottingham Arabidopsis stock center
Stanford:  Sequencing of the Arabidopsis genome at Stanford
TAIR:  Arabidopsis information resource
TIGR:  TIGR Arabidopsis genome annotation database
Wustl:  Arabidopsis genome at Washington university
Trees:  A forest tree genome database

Bacterial genomes
B. Subtilus:  Bacillus subtilus database
Chlamydomonas:  Chlamydomonas genetics center
E. coli:   E.coli genome project
MGD:  Microbial germ plasm database
Microbial:  Microbial Genome Gateway
Microbial:  Microbial genomes
Micado:  Genetics maps of B. subtilis and E. coli
MycDB:  A integrated Mycobacterial database
Neisseria:  Neisseria meningitidis genome
Neurospora:  Neurospora crassa database
OralGen:  Oral pathogen database
Salmonella: Salmonella information
STDGen:  Sexulally transmitted disease database

Bass:  Sea Bass Mapping project

Cat (Felis catus)
Cat ArkDB: Cat mapping database

Cattle (Bos taurus)
ARK: Farm animals
BoLA:  Bovine MHC information
Bovin:  Bovine genome database
BovMap:  Mapping the bovine genome
CaDBase:  Genetic diversity in cattles
ComRad:  Comparative radiation hybrid mapping
Cow ArkDB: Bovine ArkDB
GemQual:  Genetics of meat quality

Chicken (Gallus gallus)
Chicken:  Poultry gene mapping project
ChickMap:  Chicken genome project
Chicken ArkDB: Chicken database
ChickEST:  Chick EST database
Poultry:  Poultry genome project

Cotton:  Cotton data collection site

Cyano Bacteria (Blue green algae)
Cyano Bacteria:  Anabaena genome

Daphnia (Crustacea)
Daphnia pulex: Daphnia genomics consortium

Deer ArkDB:   Deer mapping database

Dictyostelium discoideum
Dicty_cDB:  Dictyostelium discoideum cDNA project
DGP:  Dictyostelium discoideum genome project
Dictybase:  Online informatics resources for Dictyostelium

Dog (Canis familiaris)
Dog: Dog genome project
Dog genome project:

Frog (Xenopus)
Xenbase:  A Xenopus web resource
Xenopus:  Xenopus tropicalis genome

Fruit fly (Drosophila melanogaster)
ENSEMBL:  Drosophila Genome Browser at ENSEMBL
Fruitfly:  Drosophila genome project at Berkeley
FlyBase: A Database of the Drosophila Genome
FlyMove:  A Drosophila multimedia database
FlyView:  A Drosophila image database

Aspergillus:  Aspergillus Genomics
Candida:  Candida albicans information page
FungalWeb: Fungi database
FGSC:  Fungal genetic stocks center

Goat (Capra hircus)
Goat:  GoatMap, mapping the caprine genome

Horse (Equus caballus)
Horse ArkDB:   Horse mapping database

Madaka Fish
Medaka:  Medaka fish home page
Maize:  Maize genome database

Malaria (Plasmodium spp)
Malaria:  Malaria genetics and genomics
PlasmoDB:  Plasmodium falciparum genome database
Parasites:  Parasite databases of clustered ESTs
Parasite Genome:   Parasite genome databases
Mosquito:  Mosquito genome web server

Mouse (Mus musculus)
ENSEMBL:  Mouse genome server at ENSEMBL
Jackson Lab:  Mouse Resources
MRC: Mouse genome center at MRC, UK
MGI: Mouse genome informatics at Jackson Labs
MGD:  Mouse genome database
MGS:  Mouse genome sequencing at NIH
MIT:  Genetic and physical maps of the mouse genome
Mouse SNP:   Mouse SNP database
NCI: Mouse repository
NIH:  NIH mouse initiative
ORNL: Mutent mouse database
RIKEN: Mouse resources
Rodentia:  The whole mouse catalog  

Pig (Sus scrofa)
INCO: Pig trait gene mapping
Pig:   Pig EST database
Pig:  Pig gene mapping project
PiGBase:  Pig genome mapping
Pig ArkDB: Pig Ark DB

PlantGDB:  Resources for plant comparative genomics

Protozoa:  Protozoan genomes

Fugu:  Puffer fish project, UK site
Fugu: Fugu genome project, Singapore
Fugu: Puffer fish project, USA

Rat (Ratus norvigicus)
MIT:  Genetic maps of the Rat genome
Rat genomics and genetics
Rat: RatMap
RGD: Rat genome database

Rice (Oriza sativa)
MPSS: Massively parallel signature sequencing
Rice-research:  Rice genome sequence database
Rice:  Rice genome project

RicBase: Rickettsia genome database

Salmon ArkDB:   Salmon mapping database

Sheep (Ovis aries)
Sheep:  Sheep gene mapping
SheepBase:  Sheep gene mapping
Sheep ArkDB:   Sheep mapping database

Soy:  Soybeans database

Sorghum:  Sorghum Genomics

Tetraodon: Tetraodon nigroviridis genome
Tetraodon: Tetraodon nigroviridis genome at Whitehead

HCGS:  Tilapia genome
Tilapia ArkDB:   Tilapia mapping database

Turkey ArkDB:   Turkey mapping database

HIV:  HIV sequence database
Herpes: Human herpes virus 5 database

Worm (Caenorhabditis elegans)
C. elegans:   C. elegans genome sequencing project
Resource for nematode sequence and functional data
WormAtlas: Anatomy of C. elegans
WormBase: The Genome and biology of C. elegans
ACEDB:  A C. elegans database
WWW Server:  C. elegans web server

SCPD:  The promoter database of Saccharomyces cerevisiae
SGD:  Saccharomyces genome database
S. Pompe:  Schizosaccharomyces pompe genome project
TRIPLES:  Functional analysis of Yeast genome at Yale
Yeast Intron database:   Spliceosomal introns of the yeast

Zebra fish (Danio rerio)
ZFIN: Zebrafish information network
ZGR:  Zebrafish genome resources
ZIS:  Zebrafish information server
Zebrafish:  Zebrafish webserver
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