RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures.
RTAnalyzer: a web application for finding new retrotransposons and detecting L1 retrotransposition signatures.
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DOI：
10.1093/nar/gkm313
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发表时间：
2007-07
影响因子：
14.9
通讯作者：
Perreault JP
中科院分区：
文献类型：
--
作者：
Lucier JF;Perreault J;Noël JF;Boire G;Perreault JP
可移动的遗传元素对哺乳动物基因组的形成有重要贡献。RTAnalyzer软件通过记录基因组内l1介导插入的特征结果来跟踪反转录起源序列。更具体地说，使用BLAST在基因组数据库中搜索感兴趣的序列。每次命中以及额外的预定义长度的5 ‘和3 ’序列都会被保存。RTAnalyzer搜索特定的L1逆转录转座特征（即目标位点复制，内切酶切割位点和poly(A)），然后计算总体逆转录转座评分。这个分数代表了一个给定序列起源于涉及L1机制的逆转录转位事件的可能性。RTAnalyzer可以在GNU公共许可下使用，并可从http://www.riboclub.org/rtanalyzer获得。
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.