te-locate a tool to locate and group transposable element occurrences using paired-end next-generation sequencing datate-locate工具来定位和组转座因子出现使用paired-end下一代测序数据.pdf

Biology 2012, 1, 395-410; doi:10.3390/biology1020395 OPEN ACCESS biology ISSN 2079-7737 /journal/biology Article TE-Locate: A Tool to Locate and Group Transposable Element Occurrences Using Paired-End Next-Generation Sequencing Data Alexander Platzer, Viktoria Nizhynska and Quan Long * Gregor Mendel Institute (GMI), Dr. Bohr-Gasse 3, 1030 Vienna, Austria; E-Mails: alexander.platzer@gmi.oeaw.ac.at (A.P.); viktoria.nizhynska@gmi.oeaw.ac.at (V.N.) * Author to whom correspondence should be addressed; E-Mail: quan.long@gmi.oeaw.ac.at; Tel.: +43-1-79044-9904; Fax: +43-1-79044-9001. Received: 27 July 2012; in revised form: 22 August 2012 / Accepted: 31 August 2012 / Published: 12 September 2012 Abstract: Transposable elements (TEs) are common mobile DNA elements present in nearly all genomes. Since the movement of TEs within a genome can sometimes have phenotypic consequences, an accurate report of TE actions is desirable. To this end, we developed TE-Locate, a computational tool that uses paired-end reads to identify the novel locations of known TEs. TE-Locate can utilize either a database of TE sequences, or annotated TEs within the reference sequence of interest. This makes TE-Locate useful in the search for any mobile sequence, including retrotransposed gene copies. One major concern is to act on the correct hierarchy level, thereby avoiding an incorrect calling of a single insertion as mult