News section

Public release PLAZA 2.5 during first week of october September 2011 (posted by Michiel Van Bel)
During the first week of october PLAZA 2.5 will be publicly released. This release contains an update to several genome annotations, as well as 2 new genomes (Strawberry and Cacao). Users of the workbench will have the option to transfer their workbench experiments from PLAZA 2.0 to PLAZA 2.5
Review Plant Comparative Genomics tools July 2011 (posted by Klaas Vandepoele)
Check out this TiPS review 'Plant protein-coding gene families: emerging bioinformatics approaches'! Includes a nice overview of several PLAZA features.
Detection orthologous genes June 2011 (posted by Michiel Van Bel)
Through the integration of a complementary set of data types orthologous gene relationships are inferred. The rationale of combining multiple approaches is to generate a consensus view of gene orthology between different species.

This new Integrative Orthology Viewer can be accessed via the Gene page and Workbench.
Apple genome published September 2010 (posted by Sebastian Proost)
The apple genome has been published in Nature Genetics. The article can be found here.

Assembly and annotation of the apple genome are included in PLAZA 2.0.
Public Release PLAZA 2.0 September 2010 (posted by Michiel Van Bel)
The second release of the PLAZA platform integrates structural and functional annotation from 23 plants covering 11 dicots, 5 monocots, 2 (club-)mosses and 5 algae (>840,000 genes). Eighty-seven percent of all protein-coding genes are stored in 32,332 multi-gene families (70% covering homologs from multiple species). Users who would like to continue working with PLAZA 1.0, please check the section Archive in the menu bar.

Disclaimer: bulk downloads are currently disabled, please use the Workbench for high-throughput sequence retrieval.
PSB Release PLAZA 2.0 July 2010 (posted by Michiel Van Bel)
The second release of the PLAZA platform integrates structural and functional annotation from 23 plants covering 11 dicots, 5 monocots, 2 (club-)mosses and 5 algae (>840,000 genes). Eighty-seven percent of all protein-coding genes are stored in 32,332 multi-gene families (70% covering homologs from multiple species).

Disclaimer: bulk downloads are currently disabled, please use the Workbench for high-throughput sequence retrieval.
Plant Cell Publication February 2010 (posted by Sebastian Proost)
The PLAZA paper has been published in Plant Cell (issue December 2009).

For more details check http://www.plantcell.org/cgi/content/abstract/21/12/3718
Update Workbench functions November 2009 (posted by Michiel Van Bel)
New features:
  • Increased the number of workbench experiments per user from 10 to 30
  • Advanced gene selection functionality: convert gene subsets (based on GO, InterPro, species or gene family) into a new workbench experiment
  • Update GO enrichment statistics

Other suggestions? Do not hesitate to contact us!
Genome Browser AnnoJ August 2009 (posted by Klaas Vandepoele)
AnnoJ has been integrated as PLAZA's Genome Browser. Currently all gene models together with a DNA sequence track are available.
Workbench activated August 2009 (posted by Michiel Van Bel)
We have developed a Workbench where for user-defined gene sets different genome statistics can be calculated. For genes sets saved by the user detailed information about functional annotations, associated gene families, block and tandem gene duplicates, and gene structure is provided. The GO enrichment tool makes it possible to determine if a user-defined gene set is over-represented for one or more GO terms. Please check the Help >> Tutorial section for more details.
Tutorials May 2009 (posted by Sebastian Proost)
Several tutorials have been added to show how the different functions of the PLAZA platform can be accessed.
The introduction covers some basics like how to find genes you're interested in. The other tutorials cover more complex topics : Gene family evolution, Genome evolution, Functional annotation and PLAZA's Workbench.

The tutorials can be found here.
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