Site Updates and News

06/27/2008 - Upgraded BLAST facility

Phytozome now employs a queuing system to handle BLAST jobs, allowing users to submit larger jobs and to be notified by email when their jobs complete. BLAST jobs can now run up to 15 minutes for email notification, and 5 minutes in interactive mode. These limits will be relaxed as resources become available (please, as a courtesy to your fellow users, no BAC blasting against unmasked assemblies at low stringency!). The BLAST results have also been recast into a more intuitive format combining the graphical and text views in a single panel. Finally, problems associated with faulty links from BLAST to Gbrowse caused by URL's with a very large number of HSPs have been resolved.

05/14/2008 - Phytozome 3.0 is here!

The latest release, v3.0, of Phytozome is now available. v3.0 expands on Phytozome v2.0 by including:

• the chromosome-based assembly and annotation of sorghum bicolor
• grape, the spikemoss Selaginella, and the algae Chlamydomonas in our ancestral gene family reconstruction, bringing Phytozome v3.0 to the Viridiplantae node of the plant evolutionary tree
• Phytozome data can now be accessed through Phytozome's BioMart application, allowing users to download gene family and individual gene sequences, annotations, and related information.

03/26/2008 - Chromosome-based assembly and annotation of Sorghum bicolor

v1.0, the first chromosome-based assembly (Sbi1) and annotation(Sbi1.4) is now available. The current Phytozome clustering still uses the v0 sorghum gene models, but we are providing access to the v1.0 browser, blast interface, and data download site here. v1.0 sorghum models will be included in Phytozome clusters in the next Phytozome release.

01/11/2008 - First look at soybean (Glycine max) assembly and annotation

A preliminary assembly and annotation of the soybean (Glycine max) genome is now available. Information and access to the data can be found here.

01/08/2008 - Minor update to Phytozome Interface

We've removed the Click-Info panel from the Cluster Summary page. The information formerly displayed there, systenic gene cluster information and PFAM domain information, is now displayed in pop-up boxes that appear when mousing over a syntenic gene or domain. To freeze the pop-up display and access the hyperlinks inside, simply click on the gene or domain image.

11/12/2007 - Composite cluster capability added to Phytozome

We've added the ability to combine the gene clusters found in single node keyword or BLAST search into a "composite" cluster that can be viewed in a cluster summary page. This is especially helpful when dealing with cases of "under-clustering," where a cohesive gene family is incorrectly broken up into several smaller clusters. Multiple sequence alignments and consensus sequences (used for BLAST searches) are calculated on-the-fly for composite clusters with fewer than 75 members. More information on this feature can be found here and here.

10/23/2007 - Minor update to Phytozome interface

Version 2.0.2 of the Phytozome website includes three new features: the ability to show search and cluster details for only those species of interest, a Get Sequences function that allow you to download gene family sequences and MSAs, and the ability to view gene family MSAs (Multiple Sequence Alignments) directly from the cluster summary page. To hide details on particular species, select the "Display" tab on the Search Results page and uncheck the species you wish to hide. You can also do the same on the "Display Options" tab on the Cluster summary page. To download gene family sequences, click on the Get Sequences tab and select the desired sequence type. To view MSAs, select the "Multiple Sequence Alignment" tab onthe Cluster summary page. For more information, please see the help page.

7/1/2007 - Two additional plant genomes added

Phytozome now includes a preliminary annotation of the grass Sorghum bicolor, as well as the version 1.1 annotation of the moss Physcomitrella patens. These genomes are joined by TIGR release 5 of the rice (Oryza sative) genome, TAIR release 6 of the Arabidopsis thaliana genome, JGI v1.1 of the poplar genome (Populus Trichocarpa), bringing to five the number of complete plant genomes analyzed in Phytozome v2.0.

7/1/2007 - New Website

A complete rework of the Phytozome website has just been completed. Navigation has been simplified, synteny viewing features have been enhanced, the individual cluster view display can be customized, and help documentation has been expanded. The genomes of individual organisms can now be searched via BLAST, and their annotations viewed within Gbrowse. In particular,

• Gbrowse genome browsers to view annotations of individual organisms (e.g, sorghum).
• BLAST search of individual genomes (e.g, Physcomitrella BLAST search), with links to Gbrowse view of results in their genomic context
• Click highlighting of orthologous syntenic genes and shared domains on cluster summary page (e.g., this cluster )
• User-configurable column display
• Ability to find all clusters containing particular sets of attributes shared with a given cluster (gene members, functional assignments)