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Nucleic Acids Research Advance Access published online on June 1, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm313
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures

Jean-François Lucier1,2,#, Jonathan Perreault1,3,#, Jean-François Noël1,2, Gilles Boire1,3 and Jean-Pierre Perreault1,3,*

1RNA Group/Groupe ARN, 2Département de microbiologie et infectiologie and 3Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada

*To whom correspondence should be addressed. Tel: +1-819-564-5310; Fax: +1-819-564-5340; Email: jean-pierre.perreault{at}usherbrooke.ca

Received February 7, 2007. Revised April 4, 2007. Accepted April 15, 2007.

Mobile genetic elements have significantly contributed to the shaping of mammalian genomes. The RTAnalyzer software tracks sequences of retrotransposed origin by scoring the signature results from an L1-mediated insertion within a genome. More specifically, a sequence of interest is searched for in genomic databases using BLAST. Each hit, along with additional 5' and 3' sequences of pre-defined lengths, is saved. RTAnalyzer searches for specific L1 retrotransposition signatures (i.e. target site duplication, endonuclease cleavage site and poly(A)), and then calculates an overall retrotransposition score. This score represents the likelihood of a given sequence originating from a retrotransposition event involving the L1 machinery. RTAnalyzer may be used under GNU public license, and is available at http://www.riboclub.org/rtanalyzer.

#The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.


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