RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures.
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.
Lucier
Jean-François
JF
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.
Perreault
Jonathan
J
Noël
Jean-François
JF
Boire
Gilles
G
Perreault
Jean-Pierre
JP
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D030561:Databases, Nucleic Acid; D005189:False Positive Reactions; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics*; D008957:Models, Genetic; D018626:Retroelements / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D020079:Terminal Repeat Sequences / Q000235:genetics*
D018626:Retroelements