Release Notes Archive

Release Notes May 2005

New Genomes Data

• Introduction of the Zea mays Accessioned BAC Browser
• Contains the 486 full-length Zea mays clones deposited with GenBank as of 31-Jan-2005
• Sequences from various grass species including rice and maize have been mapped to the BACs using the Gramene pipeline
• Gene models have been predicted using the FGENESH HMM-based ab initio gene prediction program, and their domains annotated using interproscan


• Introduction of the Zea mays Agarose FPC Map browser
• Contains 760 FPContigs imported from the AGI 25 Oct 2004 release
• Annotations, including BACs and physical markers were also imported from the AGI map. Where possible, BACend and GenBank accessions have been associated with each BAC


• Introduction of the Arabidopsis thaliana Genomes
• This is a direct copy of the Arabidopsis TIGR5 Ensembl database, kindly provided by Nottingham Arabidopsis Stock Centre


• Introduction of the Ensembl Compara database
• Putative orthologs between rice, Arabidopsis and maize gene models have been generated using Ensemb's Compara pipeline
• Syntenic regions between the maize FPC map and the rice genome assembly have been estimated, and loaded into the database

New Genomes Features

• Home page
• Saperate pages for each browsable species (Oryza sativa, Zea mays and Arabidopsis thaliana) have been created, available from a new Genomes home page


• GeneView
• A new section detailing putative orthologous genes has been added. This section carries the ID and description of each orthologue, and a link to the corresponding GeneView page


• ContigView
• Those gene models annotated with an orthologous gene in another species are now coloured blue. The popup menu for these gene models provides a direct link to the orthologous gene(s)


• CytoView
• CytoView is the default browser page for the Zea mays FPC map
• The BAC tiling path for the AGI map is displayed, with the accessioned BACs highlighted. Presence/absence of BACends is also indicated. The popup menu for each accessioned clones feature provides a link to the BAC browser
• A new track showing syntenic regions between rice and maize is shown. The feature popup can be used to jump between the species


• SyntenyView
• This new page shows the chromosome-level synteny between rice and maize, and is accessable from the species home page and the 'jump-to' menus in ContigView/CytoView

Release Notes Archive