RSAT retrieve-ensembl-seq
Returns upstream, downstream, intronic, exonic, UTR, transcript, mRNA, CDS or gene sequences for a list of genes from the EnsEMBL database.
Multi-genome queries are supported: automatic retrieval of sequences for all the orthologs of the query genes, at a given taxonomical level.
Topics
Collections
Details
- License:
- AFL-3.0
- Maturity:
- Mature
- Cost:
- Free of charge
- Tool Type:
- api, command-line tool, web application
- Operating Systems:
- Linux, Mac
- Programming Languages:
- Perl
- Added:
- 12/13/2019
- Last Updated:
- 6/16/2020
Operations
Data Inputs & Outputs
Data retrieval
Publications
PMID: 19720677
Documentation
API documentation
http://pedagogix-tagc.univ-mrs.fr/rsat/htmllink.cgi?title=RSAT%20:%20Web%20services%20documentation&file=web_services/RSATWS_documentation.xmlDocumentation for the SOAP/WSDL Web services
Installation instructions
https://rsa-tools.github.io/installing-RSAT/Training material
https://teaching.rsat.eu/tutorials/tut_retrieve-ensembl-seq.htmlDownloads
- Biological datahttps://github.com/rsa-tools/motif_databasesKnow transcription factor binding motifs imported from a wide variety of databases
- Container filehttps://biocontainers.pro/#/tools/rsat-core
- Downloads pagehttp://download.rsat.eu/
- Source codehttps://github.com/rsa-tools/rsat-code.gitTo obtain a git clone, run the command "git clone [this_url]. To get updates, cd to the rsat-code folder and run "git pull".
- Source codehttps://github.com/rsa-tools/rsat-code/releasesCompressed archives for each RSAT release
- Test datahttps://github.com/rsa-tools/demo_filesDemo files
- Test scripthttps://raw.githubusercontent.com/rsa-tools/rsat-code/master/makefiles/subcommand_tests.mk
Links
Service
http://prokaryotes.rsat.eu/retrieve-ensembl-seq_form.cgi(Prokaryote-specific RSAT instance – includes Bacteria and Archaea)
Issue tracker
https://github.com/rsa-tools/rsat-code/issuesRelated Tools
rsat
Relation: includedIn