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

Lucier, Jean-François; Perreault, Jonathan ORCID: https://orcid.org/0000-0003-4726-6319; Noël, Jean-François; Boire, Gilles et Perreault, Jean-Pierre (2007). RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures Nucleic Acids Research , vol. 35 , nº Web Serv. w269-w274. DOI: 10.1093/nar/gkm313.

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Résumé

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.

Type de document:	Article
Mots-clés libres:	-
Centre:	Centre INRS-Institut Armand Frappier
Date de dépôt:	04 nov. 2024 20:37
Dernière modification:	04 nov. 2024 20:37
URI:	https://espace.inrs.ca/id/eprint/14922

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