PLAZA 4.0 is the latest iteration of the PLAZA framework consisting of two instances: Dicots 4.0 and Monocots 4.0. The total number of species across both instances nearly doubled from 37 species in PLAZA 3.0 to 71 species in PLAZA 4.0, with a much broader coverage of crop species (e.g. wheat, palm oil) and species of evolutionary interest (e.g. spruce, Marchantia).

New features include

• New and improved visualizations for multiple sequence alignments, phylogenetic trees (PhyD3) and gene collinearity (interactive WGDotplot & SyntenyPlot)
• An Interactive Phylogenetic Module allowing users to create custom phylogenetic trees by using the PLAZA platform as reference
• Access by an application programming interface (API) through a RESTful web service
• Improved management of Workbench experiments between different users

If you notice bugs or issues, feel free to contact us.

Due to security concerns all PLAZA instances will now automatically make use of the secure http protocol (https).

Based on our recent paper 'A Collection of Conserved Non-Coding Sequences to Study Gene Regulation in Flowering Plants' (Van de Velde et al., 2016), PLAZA Dicots 3.0 now hosts conserved transcription factor (TF) binding site information for >600 TFs. Apart from identifying for any TF target genes with a conserved binding site in ten different species, also the associated gene families and Gene Ontology/InterPro annotations can be browsed. Reversely, for every gene the conserved TF binding sites in the upstream/intron/downstream non-coding can also be retrieved.
The TF binding sites are available for the following species: Arabidopsis thaliana, Brassica rapa, Populus trichocarpa, Glycine max, Prunus persica, Cucumis melo, Eucalyptus grandis, Vitis vinifera, Solanum lycopersicum, Solanum tuberosum

For more examples, please see our tutorial Browsing conserved TF binding sites.

Dear PLAZA users,

we want to inform you that we identified and corrected a software bug in one of the tools used in PLAZA 3.0 to compute integrative orthology.
Specifically, for the Best-Hits-and-Inparalogs (BHI) method, we found that while the Best Hits in other species were correctly scored, inparalogs were not correctly identified. This means that no genes were incorrectly identified as being orthologous, but that some orthologs might have been missed (no false positives, some false negatives).

This issue has now been resolved and the data in he PLAZA 3.0 Dicots and Monocots databases and the corresponding FTP download sections have been updated.

Apologies for any inconvenience caused, The PLAZA team

We want to inform you that the PLAZA 3.0 Monocots website has been updated, now including additional integrative orthology information for Oryza sativa (osa). Downstream data types, incl. orthology-based GO projection as well as the functional annotations for Monocots 3.0 Workbench experiments, have also been updated.

Dear,

We want to inform you that the PLAZA 3.0 websites will be unavailable Friday 12 December 2014, between 12-14h CET.

We will perform some maintenance operations fixing missing bootstrap values in the phylogenetic trees as well as updating depending data types.

For all PLAZA 3.0 Workbench users, the functional gene annotations of your experiments will be automatically updated. Note that some minor differences in gene functions might occur due to the orthology-based projection.

Apologies for any inconvenience caused by these operations.

Best regards, the PLAZA team

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.

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

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' or check this example!

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.

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

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.

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.

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.

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.

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.

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

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!

AnnoJ has been integrated as PLAZA's Genome Browser. Currently all gene models together with a DNA sequence track are available.

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.