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Bioinformatics Advance Access originally published online on August 31, 2009
Bioinformatics 2009 25(20):2739-2740; doi:10.1093/bioinformatics/btp519
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl

Olivier Sand *, Morgane Thomas-Chollier and Jacques van Helden

Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles CP 263, Campus Plaine, Boulevard du Triomphe, B-1050 Bruxelles, Belgium

* To whom correspondence should be addressed.


  Abstract

Summary: The preparation of an appropriate sequence dataset is the starting point of all genomic analyses. We present retrieve-ensembl-seq, an application that considerably eases the retrieval of sequences from the Ensembl database, via our user-friendly web site or web services. The user provides Ensembl identifiers or gene names, and the program returns corresponding upstream, downstream, intronic, exonic, UTR or whole gene sequences. retrieve-ensembl-seq also offers a multiple organism mode to retrieve sequences from homologous genes at any taxonomical level. And we introduce various original filters such as the masking of coding fragments and the avoidance of sequence redundancy for genes with multiple transcripts. retrieve-ensembl-seq is included in the software suite regulatory sequence analysis tools (RSAT), allowing instant submission of retrieved sequences to further analysis tools.

Availability: retrieve-ensembl-seq is integrated in the RSAT suite: http://rsat.ulb.ac.be/rsat. Web site: http://rsat.ulb.ac.be/rsat/retrieve-ensembl-seq_form.cgi. Web services: http://rsat.ulb.ac.be/rsat/web_services/RSATWS.wsdl. Stand-alone distribution: freely available under an academic licence to download from the RSAT web site. The complete manual, a convenient tutorial and demos are available from the RSAT website. Additional help can be found on the RSAT public forum.

Contact: oly{at}bigre.ulb.ac.be

Associate Editor: Dmitrij Frishman

Received on May 25, 2009; revised on August 25, 2009; accepted on August 25, 2009

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