News section

Building PLAZA 3.0 December 2013 (posted by Sebastian Proost)
We are currently in the process of building PLAZA 3.0. This upcoming release will include several new species like tomato, potato, rapeseed, ... While building a new plaza release there is a considerable extra load on the database. Because of this the website might respond slower. This is only temporary.
Thank you for participating in the PLAZA survey. March 2013 (posted by Michiel Van Bel)
We would like to express our gratitude to everyone who participated in the PLAZA survey. If you have any more questions or remarks, you can send them plaza@psb.vib-ugent.be
View all colinear gene pairs August 2012 (posted by Klaas Vandepoele)
We have added a new feature on the Gene page to rapidly explore all colinear gene information across species. See the function 'View all colinear gene pairs'.
PLAZA 3.0 roadmap April 2012 (posted by Michiel Van Bel)
The PLAZA team is currently working towards the 3.0 release of the PLAZA platform and we're looking for user input! What new genomes and features would you like to see incorporated? Are there any other improvements that you would like to see? Contact us at plaza@psb.ugent.be.
PLAZA is tip of the week on openhelix December 2011 (posted by Michiel Van Bel)
From openhelix.org:

"Plaza, a resource for plant comparative genomics, has a lot more than meets the eye at first. Currently the database has comparative tools and data for nearly 2 dozen plants including monocots, dicots, mosses and algae..."

Read more and view the video on Openhelix
PLAZA 2.5 online September 2011 (posted by Michiel Van Bel)
The third release of the PLAZA platform, designated version 2.5, is currently available. New genomes include strawberry (Fragaria) and cacao (Theobroma) while several other species, like Arabidopsis thaliana, Zea mays and Brachypodium distachyon, have been updated.

The current release includes >900,000 genes from 25 species, yielding 22,350 multi-species gene families.

New tools include the Circle Plot, a multi-species WGDotplot, a Gene Family Finder, Expansion Plot, and an Integrative Orthology Viewer to explore orthologous genes in other species by combining different orthology prediction methods.

Workbench experiments from PLAZA 2.0 can be transferred to PLAZA 2.5.
Detection orthologous genes December 2010 (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 tool 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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