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Nucleic Acids Res. 2007 Jul;35(Web Server issue):W269-74. Epub 2007 Jun 1.

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

Author information

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

Abstract

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.

PMID:
17545202
PMCID:
PMC1933146
DOI:
10.1093/nar/gkm313
[Indexed for MEDLINE]
Free PMC Article

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