Frequently Asked Questions
Platform & Annotations
Previous versions of the PLAZA platform are still available and can be reached using Menubar→Version (cfr. dicots 3.0, top right next to the search bar). Older versions are no longer modified in terms of data & tools. In contrast, Workbench experiments containing user-defined gene sets are still fully operational and are maintained independently per PLAZA version.
Current supported web browsers:
Recent versions Apple Safari should work as well, but are currently not tested.
Some parts of the site look scrambled/different compared to the screenshots/tutorial.
Make sure you are using a recent version of one of the supported browsers*
If the problem still persists, please send a bug report detailling your current setup and a clear description (possibly with a screenshot) of the broken view within the website.
From PLAZA 4.0 on, the platform no longer relies on external plugins (such as Flash or Java), these plugins should no longer cause issues. Older versions of PLAZA however, might be still reliant on these plugins.
I think I found an error/bug!
Please use the contact information at the bottom of each page to let us know. Please note that, unless severe issues are discovered, that we only support bugfixes for the latest PLAZA instances.
If you have used PLAZA for your research and would like to cite it in your paper, please use one of these references listed on this page:PLAZA publications
Linking to gene pages within the PLAZA platform
Several PLAZA instances exist within the PLAZA platform, each with its own URL. You can either link directly to a specific instance, or link to overview website of the PLAZA platform which should then redirect to the correct PLAZA instances
To link directly to a gene-page on a specific PLAZA instance, the only information needed is the PLAZA instance URL, and a recognized PLAZA gene identifier. The URL needs to be constructed as such:
- Example: https://bioinformatics.psb.ugent.be/plaza/versions/plaza_v4_development/genes/view/Brara.C00993
Because it is not always clear which gene identifiers PLAZA uses (in cases various identifiers are defined for a single gene/locus), it is sometimes better to rather let the platform search the database for recognized gene identifiers. If the PLAZA platform then recognizes the provided identifier, the user will be redirected to the correct gene page. The template URL for this page looks like this:
- Example: https://bioinformatics.psb.ugent.be/plaza/versions/plaza_v4_dicots/genes/locate_gene/zma/GRMZM2G111782
The previous solutions all require you to know the PLAZA instance you want to target, the mapping from organism to PLAZA species name, the used naming scheme for PLAZA gene identifiers, or a combination of such. We recognize this is not an optimal situation, and therefore offer a more integrated solution, relying on the PLAZA platform to redirect incoming links to the possible PLAZA instances. The only requirements here are that the incoming link contains any type of identifier, and the taxonomy ID (see NCBI taxonomy) for the species the identifier belongs to. The use of the taxonomy identifiers ensures that the websites linking to PLAZA don't need to know any of the internal name mappings used by the PLAZA platform. The template URL for this redirect tool looks like this:
In case that there are still uncertainties about how the link to the PLAZA website, please contact the site administrator.
How is the species tree created?
Currently, the PLAZA species tree is manually constructed using information from the National Center for Biotechnology Information taxonomy (Federhen, 2011), with additional information from the literature to resolve trifurcations. More information can be found in the supplementary data associated with the publication for each PLAZA release.
Platform & Annotations
Why is genome X not included in your platform ?
We make a selection from the publicly available plant genomes based on the quality of the assembly and annotation, as well as the coverage per phylogenetic clade. More information can be found the in the publications for each PLAZA release.
Unpublished annotation releases
Our general policy is to rely on community annotations as much as possible, and this for two reasons. Firstly, these (frequently published) official releases are most of the time considered as 'the reference' for a given model species, making linking to generally accepted gene identifiers straightforward. Secondly, although we realize that some of these public annotations are far from perfect (see section Construction for more information about Quality Control), we suggest users to directly contact community annotation providers (or the PI of a specific genome project) in case they can provide better genome annotations. The PLAZA team does not have the means to re-annotate complete plant genomes, so contacting annotation providers is probably the best way to distribute new annotations to the scientific community (and get these improved annotation in future PLAZA versions). As a side note, please consider that objectively demonstrating that your annotation is superior to a public reference annotation is probably an important criterion.
I like this platform, can I set up a PLAZA version for myself with different organism?
Currently, there are no plans to publicly release the platform in such way it can be deployed on other systems. Please contact us for more information or collaborations.
Check Data→Download to download tab-delimited data files containing structural and functional annotation data, as well as sequence data. Please also see our FTP directory ftp://ftp.psb.ugent.be/pub/plaza/.
Apart from coding and amino acid gene sequences, it is also possible to retrieve non-coding DNA sequences (e.g. upstream or downstream). These sequence types are accessible via the Gene Page→Show Sequences or via the Workbench→Export function.
The re-distribution of large-scale PLAZA comparative genomics datasets through other online databases is not permitted, please contact us for more information.
In the Synteny plot it seems similar segments are nott next to each other...
The clustering of the gene strings, that determines the order, is done with the maximum window size (15 genes left and right). Sometimes, when viewed with a window size of 5 genes, this gives the impression similar regions are not grouped together. Use the zoom option and reinspect the plot.
Why do chromosomes contain less genes in the WGDotplot then in the actual annotation?
This is a consequence of the detection using i-ADHoRe. i-ADHoRe remaps tandem duplicates onto a representative: tandem duplicates that are not representatives are then removed from the genelists as they have a negative influence on the colinearity detection. All output generated is based on these remapped genelists and therefore lacks some genes that were duplicated by tandem duplications.
Why are some genes both Tandem and Block duplicates?
i-ADHoRe, the tool used to detect genomic homology, first identifies tandem duplicates (i.e. homologous genes in close proximity) before detecting homologous regions. During tandem detection, all genes within a tandem array are remapped/collapsed on a tandem representative. Consequently, when such a tandem representative is a block duplicate within a colinear region, multiple duplication events most probably shaped the genomic region under investigation. Therefore, we also flag all genes within the original tandem array as block duplicates.
What organisms should I select when using the Skyline plot or WGDotplot?
When selecting the species included you should aim to include all species you're interested in, but as few as possible other species.
Where can I download Ks values ?
First generate a WGDotplot for the species (or two species) you need Ks values for. At the bottom of the page (below the Ks distribution) there is a button to download Ks values for all pairs in the plot.
When running GO enrichment, what GO source should I use?
- Primary GO data refers to annotations made by the GO consortium, UniProtKB/Swiss-Prot or found using InterProScan.
- 'Primary and Orthology' comprises primary + orthology-based transfer (iOrtho and reconciled phylogenetic trees)
- 'All' covers Primary + Orthology- + Homology-based transfer.
The Orthology-based method only transfers primary annotations based on experimental GO evidence codes while Homology-based transfer gene family GO annotations to the individual gene family members. Although the gene-GO coverage is all»homology»orthology>primary, GO annotations from homology- and orthology-based transfer are purely electronic. For more details, please see the PLAZA 3.0 paper, Supplementary Method 1: Projection of GO annotation.