Each user has the ability to create up to 20 different TRAPID experiments.
Go to the forgotten password page and fill in the form with the email address used to create a TRAPID account to reset your password. If this does not work, contact us and we will send you a new password for your user account.
Please do. Just send us an email, and we will investigate the issue.
Yes. We have taken extensive measures to ensure that only authorized people have access to the user data.
TRAPID is freely accessible for academic use exclusively. If you have a commercial interest in the platform, or would like to use TRAPID for commercial purposes, please contact Klaas Vandepoele.
In case you publish results generated using TRAPID, please cite this paper:
If you cite results based on third-party resources used by TRAPID (e.g. taxonomic classification, phylogenetic trees), please cite the appropriate papers as well. More information about this can be found in tools & parameters.TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes
Francois Bucchini, Andrea Del Cortona, Łukasz Kreft, Alexander Botzki, Michiel Van Bel, Klaas Vandepoele
Nucleic Acids Research, 01 July, 2021
TRAPID supports correctly formatted FASTA files, with the > symbol indicating the transcript identifier of the following sequence. In case the headers of the file consist of multiple sections separated by the | symbol (pipe), the first section will be used as unique identifier. Please note that TRAPID works with nucleotide sequences exclusively.
Several online resources are available to help users perform sequence assembly and prepare their data for use with TRAPID. More information can be found in the general documentation.
TRAPID is able to process up to 200,000 transcripts within a single experiment. Adding more transcripts is possible, but correct processing or website performance is not guaranteed in this case.
Within a TRAPID experiment, click Import data in the side menu. There, choose Transcript subset. You can then upload a file containing the list of transcript ids for the subset, and choose a name for the subset. Finish by clicking Import subset.
Yes you can. Within a TRAPID experiment, click Export data to go to the export page. More information about the content and format of exported files can be found in the general documentation.
You can. In case you do, we recommend to either make use of the taxonomic classification functionality of TRAPID (ensure this step is enabled during initial processing), or to use subsets to mark the origin of different transcripts (e.g. from species X and Y). Note that you easily can upload multiple sequence files into one experiment; see the general documentation for more information.
We offer four reference databases: the latest PLAZA databases (PLAZA dicots and monocots 4.5, pico-PLAZA 3), and EggNOG 4.5. In case you are working with data originating from plants or algae, we recommend using the most suited PLAZA instance (i.e. that contains genomes from closely related species). In case data from other lineages is analyzed, we recommend selecting EggNOG 4.5. An overview of the content of the various reference databases can be found in the tools & parameters documentation page.
All third-party resources used by TRAPID are listed in the tools & parameters page, along with version and parameters information.
After the multiple sequence alignment (MSA) or phylogenetic tree has been created for a given gene family, the user can download the MSA in .faln (fasta) format, or the phylogenetic tree in newick and phyloXML format, by following the download links provided in the Files & extra tab of the MSA/tree page.
Due to the heavy computational requirements for generating multiple thousands of multiple sequence alignments and phylogenetic trees, this is currently not possible. As such, creating phylogenetic trees can only be done on a per-gene family basis.