Genome Analysis
Model Organism Databases
- AMPDB: Arabidopsis Mitochondrial Protein Database
Search for information on the predicted and experimentally confirmed protein complement of mitochondria from the model plant Arabidopsis thaliana
- CATMA: Complete Arabidopsis Transcriptome MicroArray
The design and production of high quality Gene-specific Sequence Tags (GSTs) covering most Arabidopsis genes. The GST collection is used by numerous groups for the production of DNA arrays for transcript profiling experiments
- FLAGdb++
Search and visualize data for high-throughput functional analysis of Arabidopsis, rice, and other plant genomes
- GénoPlante-Info (GPI)
Search for genomic information on five major crop species (corn, wheat, rapeseed, sunflower seed and pea crops) and and model plants (Arabidopsis and rice)
- MatDB
Contains all Arabidopsis sequences and annotation produced by the Arabidopsis Genome Initiative, plus the mitochondrial and chloroplast genomes
- SeedGenes Project
Search for molecular and phenotypic information on essential, non-redundant genes of Arabidopsis that give a seed phenotype when disrupted by mutation
- TAIR: The Arabidopsis Information Resource
Includes a searchable relational database, which includes many different datatypes. It also includes information about the Arabidopsis Genome Initiative, lab protocols, and other links
- TIGR Arabidopsis Genome Annotation Database
Go back to top
- C. elegans Mitochondrial Directory
A list of genes which encode mitochondrially localised proteins
- C. elegans Oligo Primer Database
Oligos for predicted C. elegans at C. elegans Knockout Consortium site
- C. elegans Repeat Families
Repeat sequences characterised from the C.elegans genome
- Ensemble C.elegans
Explore the Caenorhabditis elegans genome
- Intronerator
Web-based tools for exploring RNA splicing and gene structure in C. elegans
- NCBI Nematode Genome Resources
Offers a gateway to nematode genome resources at NCBI and beyond
- RNAiDB
RNAi phenotypic analysis of C. elegans genes
- WorfDB
Search for availability and quality of cloned ORFs in Caenorhabditis elegans
- WormBase
Provides accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and some related nematodes
- WormBook
The Online Review of C.elegans Biology, includes an up-to-date collection of methods and protocols for C. elegans researchers
- Wormpep
Contains the predicted proteins from the Caenorhabditis elegans genome sequencing project
Go back to top
- Dicty BLAST
Provides BLAST search access to all the Dictyostelium discoideum sequence information (shotgun reads, contigs, ESTs, GenBank submissions, gene model translations
- Dicty Genome Project
Portal for access to Dictyostelium genome information
- Dicty Workbench
Provides a comprehensive Dictyostelium discoideum genome annotation and analysis portal
- DictyBase
Provides a single portal for access to Portal for access to Dictyostelium genome information
- DictyDB Loci and Genetic Maps
Genetic and physical maps for the six Dictyostelium chromosomes
- DictyOGlyc
Produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins
- NCBI Dictyostelium Genome Resources
Provides one-click links to Dictyostelium-related resources at NCBI and pathways out to additional resources available to the research community
- NIH Dicty
Portal for access to Dictyostelium genome information
Go back to top
- DPDB
Drosophila polymorphism database
- Drosophila RNAi
RNAi screening center at Harvard.
- Ensembl Fruitfly
Explore the Drosophila melanogaster genome
- FLIGHT
Drosophila phenotypes, gene expression and protein interaction data
- FlyBase
Genetic and molecular data for Drosophila
- FlyBase BLAST
BLAST the Drosophila Genome
- FlyBrain
Database of the Drosophila nervous system
- Flynet
Build a network from Drospophila protein-protein interactions detected experimentally or mapped cross-species from Saccharomyces orthologs
- Flytrap
Search and visualize protein localization
- FlyView
Drosophila development and genetics (German)
- Fruitfly
Berkeley Drosophila Genome Project
- Homophila
A tool for planning functional genomic investigations in Drosophila that address questions about genetic disease in humans
- MitoDrome
Search for information on nuclear genes encoding proteins involved in mitochondrial biogenesis and function
- NCBI Drosophila Genome Resources
Brings together information on Drosophila-related resources from NCBI and the fruit fly research community
Go back to top
- coliBASE
Study comparative genomics of Escherichia coli, Shigella and Salmonella
- Colibri
E. coli genome database at Institut Pasteur
- DPInteract Compilation Paper
Binding sites for E. coli DNA-binding proteins
- E. coli Genome Project
E. coli K-12 sequence and annotations
- E.coli Genome Project (EHEC)
Enterohaemorrhagic Escherichia coli (EHEC) O157:H7
- EchoBASE
Search for comprehensive genetic information and experimental results of Escherichia coli K-12
- EcoCyc
Search for comprehensive biological information on bacterium Escherichia coli K12 MG1655
- EcoGene/EcoWeb
EcoGene is a collection of information about the genes, proteins, and intergenic regions of the E. coli K-12 genome and proteome
- GenoBase
E. coli genome database at Nara Institute
- GenProtEC
E. coli genome and proteome
- PEC: Profiling of E. coli Chromosome
Comprehensive database on E. coli genome
- PromEC
E. coli mRNA promoters with experimentally identified transcriptional start sites
- RegulonDB
Search for experimental knowledge about the elements and interactions of the transcriptional regulation network in Escherichia coli K-12
Go back to top
- Mycoplasma mobile Database
Contains information about biochemical reactions, their compounds and the pathways in which they participate, all this related to information on proteins, genes, enzymes and organism
Go back to top
- RAD: Rice Annotation Database
Contig-oriented database for high-quality manual annotation of RGP, which can present non-redundant contig analyses by merging the accumulated PAC/BAC clones
- RGP
Portal for Rice Genome Research Program
- RiceBLAST
Rice sequence database BLAST search
- RiceGAAS: Rice Genome Automated Annotation System
Search for reliable and up-to-date analysis of the rice genome sequence as well as to store and retrieve the results of annotation
- RiceHMM
Predicts gene domains on rice genome sequence based on probabilistic model using a catalog of rice ESTs
- RISe
Integrated information resource and comparative analysis workbench for rice genomics
- TIGR Rice Genome
Provides sequence and annotation data for the rice genome
Go back to top
- FYSSION
Functional genomics of fission yeast
- Schizosaccharomyces pombe GeneDB
Contains all S. pombe (fission yeast) known and predicted protein coding genes, pseudogenes, transposons, tRNAs, rRNAs, snRNAs, snoRNAs and other known and predicted non-coding RNAs
Go back to top
- AxelDB
Database focussing on gene expression in the frog Xenopus laevis
- NCBI Xenopus Genome Resources
Bring together information on
Xenopus laevis and Xenopus tropicalis
tools at NCBI and Xenopus community related resources
- XDB3
Web data catalogue of NIBB/NIG/NBRP Xenopus laevis EST project
- Xenbase
Information pertaining to the cell and developmental biology of the frog, Xenopus
Go back to top
- MAGI
Results of a maize genome assembly project
- Maize Targeted Mutagenesis Database
Transposon library in maize for the purpose of targeted selection of gene knockouts
- MaizeGDB
Search genetic and genomic information about Maize
- MaizeSeq
Pioneer, Monsanto, and Ceres have made maize sequences available to non-profit organizations
- Panzea
Contains the genotype, phenotype, and polymorphism data produced by the Molecular and Functional Diversity in the Maize Genome project (NSF)
- TIGR Maize
Numerous tools for investigating the maize genome, including tools for browsing BACs as well as a full gene index
Go back to top