Gramene

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