Research guides: BIO372H5: Molecular Biology: Genome Databases

Organism Specific

FlyBase
FlyBase, a database dedicated exclusively to Drosophila genes and genomes, includes information on 12 species of Drosophila.
The Arabidopsis Information Resource (TAIR)
TAIR contains information specific to Arabidopsis thaliana, including intron-exon structure, intron lengths, and alternative splicing.
Soybase
Soybase, the Soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean.
Nematostella vectensis v1.0 - JGI Genome Portal
Nematostella vectensis genomic database.
Mouse Genome Informatics (MGI)
The international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.
E. coli Gene Expression Database (GenExpDB)
The Rat Genome Database (RGD)
This database aims to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community.
The Zebrafish Model Organism Database (zfin)
Wormbase
The Caenorhabditis elegans genome database.
NEMBASE
A comprehensive Nematode Transcriptome Database.
Xenbase
A comprehensive, integrated and easy to use web based resource that gives access the diverse and rich genomic, expression and functional data available from Xenopus research.
wFleaBase
Gene and genomic information for species of the genus Daphnia - commonly known as the water flea.
Saccharomyces Genome Database (SGD)
Cyanobacteria - JGI Genome Portal

Multiple Organism

Genome
Genome-related information for the following organisms: Archaea, Bacteria, Eukaryotae, Viruses and Viroids. Also included are completed chromosomes, organelle and plasmid data
Sanger Institute Model Organisms Genomes
The Sanger Institute provides links to resources for model organisms, including whole genomes for the: mouse, zebrafish (Danio rerio), worm (Caenorhabditis elegans), frog (Xenopus tropicalis) and yeast (Saccharomyces pombe, S. paradoxus and S. cerevisiae).
Salad
The Surveyed conserved motif ALignment diagram and the Associating Dendrogram database is a genome-wide database of similarity clustering based on distribution patterns found in proteome datasets of rice, sorghum, Arabidopsis thaliana, grape, a lycophyte, a moss, algae, and yeast.
Plant Transcription Factor Database (PlnTFDB) (3.0)
A public database arising from efforts to identify and catalogue all Plant genes involved in transcriptional control.
PlantGDB
Tools and resources for plant genomics.
Gramene
A curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species.
Human Genome Epidemiology (HuGE) encyclopedia
An integrated, searchable knowledge base of genetic associations and human genome epidemiology.
Wellcome Trust Sanger Institute
As one of the largest sequencing centres in the world for more than 15 years, the Wellcome Trust Sanger Institute has produced more than 100 finished genomes.
Ensembl Genome Browser
Ensembl is a joint project between EMBL - EBI and the Wellcome Trust Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes.

SimGene

This application interfaces with Simbiot, Ensembl, NCBI, Gene Ontology, KEGG Pathways, PubMed, Genomic Variations and many other databases to retrieve up-to-date annotation information for over 30 species, based on gene symbol search. The application provides gene and transcript cross reference information for NCBI, Ensembl, RefSeq and UniProt. SimGene also contains an integrated genome browser with information on genes, transcripts, exons and SNPs.