LTR_STRUC: a novel search and identification program for LTR retrotransposons
LTR_STRUC: a novel search and identification program for LTR retrotransposons
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DOI：
10.1093/bioinformatics/btf878
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发表时间：
2003-02-12
期刊：
影响因子：
5.8
通讯作者：
McDonald, JF
中科院分区：
文献类型：
--
作者：
McCarthy, EM;McDonald, JF
动机：长末端重复（LTR）逆转录转座子构成了大多数真核生物基因组的很大一部分，并且被认为对基因组的结构和功能有重要影响。在基因组数据库中搜索LTR反转录转座子的传统方法是劳动密集型的。我们提出了一种高效、可靠和自动化的方法来识别和分析这类重要的转座元件。结果：我们开发了一个新的数据挖掘程序LTR- struc （LTR逆转录转座子结构程序），该程序通过搜索基因组数据库中LTR逆转录转座子的结构特征来识别和自动分析这些元件。LTR- struc在与已知查询序列同源性较低的LTR反转录转座子家族或非典型结构家族（例如缺乏典型逆转录病毒orf的非自主元件）的情况下，比传统搜索方法具有显著优势，因此是一种补充现有方法的发现工具。LTR- struc使用一种算法发现LTR反转录转座子，该算法包含许多任务，否则必须由用户单独启动。对于每一个发现的LTR反转录转座子，LTR- struc都会自动生成一系列具有生物学意义的结构特征分析。
Motivation: Long terminal repeat (LTR) retrotransposons constitute a substantial fraction of most eukaryotic C, genomes and are believed to have a significant impact on genome structure and function. Conventional methods used to search for LTR retrotransposons in genome databases are labor intensive. We present an efficient, reliable and automated method to identify and analyze members of this important class of transposable elements.Results: We have developed a new data-mining program, LTR-STRUC (LTR retrotransposon structure program) which identifies and automatically analyzes LTR retrotransposons in genome databases by searching for structural features characteristic of such elements. LTR-STRUC has significant advantages over conventional search methods in the case of LTR retrotransposon families having low sequence homology to known queries or families with atypical structure (e.g. non-autonomous elements lacking canonical retroviral ORFs) and is thus a discovery tool that complements established methods. LTR-STRUC finds LTR retrotransposons using an algorithm that encompasses a number of tasks that would otherwise have to be initiated individually by the user. For each LTR retrotransposon found, LTR-STRUC automatically generates an analysis of a variety of structural features of biological interest.