Announcing Gramene Release 17a

[Shuly Avraham]

We are pleased to announce the release of Gramene version 17a.

This is an 'interim' release, and only the Genome Browser data and
software have been updated.

New Genome Browser 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 Genome Browser;

   - 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 Genome Browser Features
***************************
- Home page;

   - Saperate pages for each browsable species (Oryza sativa, Zea mays
     and Arabidopsis thaliana) have been created, available from a new
     Genome Browser 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.