Applied Bioinformatics Course

List of genome databases

• GOLD - Genomes Online Database, a comprehensive information resource for complete and ongoing genome sequencing projects with flowcharts and tables of statistical data. Created and maintained by
• Karyn's Genome - A collection of sequenced genomes with brief description and references for each genome. The direct links to the sequence data in EMBL or annotations in ENSEMBL make it very convenient for the user community.
• CropNet - The website of the UK Crop Plant Bioinformatics Network to the development, management, and distribution of information relating to comparative mapping and genome research in crop plants.

Genome browsers and analysis platforms

• NCBI Genome - The entry portal to various NCBI genomic biology tools and resources, including the Map Viewer, the Genome Project Database and the Plant Genomes Central, etc.
• GoldenPath - The genome browser website containing the reference sequence and working draft assemblies for a large collection of genomes at the University of California at Santa Cruz (UCSC).
• ENSEMBL - The web server of the European eukaryotic genome resource developed by EBI and the Sanger Institute. [PDF]
• VISTA - A comprehensive suite of programs and databases for comparative analysis of genomic sequences.
• TIGR Plant Genomics - TIGR plant genome databases and tools.
• TIGR Gene Indices - TIGR gene indices maintained at Harvard.

Genome database of model organisms

• Gramene - A curated open-source data resource for comparative genome analysis in the grasses including rice, maize, wheat, barley, sorghum etc, as well as other plants including arabidopsis, poplar and grape. Cross-species homology relationships can be found using information derived from genomic and EST sequencing, protein structure and function analysis, genetic and physical mapping, interpretation of biochemical pathways, gene and QTL localization and descriptions of phenotypic characters and mutations.
• TAIR - The Arabidopsis information resource maintained by Stanford University. It includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community.
• AtENSEMBL - A genome browser for the commonly studied plant model organism Arabidopsis thaliana.
• Oryzabase - A comprehensive rice science database maintained by National Institute of Genetics, Japan. It contains genetic resource stock information, gene dictionary, chromosome maps, mutant images and fundamental knowledge of rice science.
• Flybase - A comprehensive database of drosophila genes and genomes maintained by Indiana University.
• CyanoBase - The genome database for cyanobacteria developed by Kazusa Institute, Japan.