IMEx: Imperfect microsatellite extractor
IMEx: Imperfect microsatellite extractor
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DOI：
10.1093/bioinformatics/btm097
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发表时间：
2007-05-15
期刊：
影响因子：
5.8
通讯作者：
Nagarajaram, Hampapathalu A.
中科院分区：
文献类型：
--
作者：
Mudunuri, Suresh B.;Nagarajaram, Hampapathalu A.
动机：微卫星，也称为简单序列重复，是迄今为止在每个已知基因组中发现的大小为 1-6bp 的核苷酸基序的串联重复。它们在基因组中的重要性是众所周知的。微卫星与多种疾病基因相关，已被用作连锁分析和DNA指纹研究中的分子标记，并且似乎在基因组进化中发挥着重要作用。因此，研究感兴趣基因组中微卫星的分布、富集和多态性具有重要意义。为此，先决条件是有一个计算工具可以从整个基因组序列中提取微卫星（完美的和不完美的）及其相关信息。对现有工具的检查揭示了其中的某些缺陷，并促使我们开发一种新工具。 结果：为了有效筛选基因组序列中的微卫星（完美和不完美），我们开发了一种称为 IMEx（不完美微卫星提取器）的新工具。 IMEx 使用简单的字符串匹配算法和滑动窗口方法来筛选 DNA 序列中的微卫星，并报告基序、拷贝数、基因组位置、附近基因、突变事件和许多其他有助于深入研究的特征。 IMEx 比现有的广泛使用的工具更灵敏、更高效、更有用。 IMEx 可以以独立程序的形式以及网络服务器的形式使用。
Motivation: Microsatellites, also known as simple sequence repeats, are the tandem repeats of nucleoti de motifs of the size 1-6bp found in every genome known so far. Their importance in genomes is well known. Microsatellites are associated with various disease genes, have been used as molecular markers in linkage analysis and DNA fingerprinting studies, and also seem to play an important role in the genome evolution. Therefore, it is of importance to study distribution, enrichment and polymorphism of microsatellites in the genomes of interest. For this, the prerequisite is the availability of a computational tool for extraction of microsatellites (perfect as well as imperfect) and their related information from whole genome sequences. Examination of available tools revealed certain lacunae in them and prompted us to develop a new tool.Results: In order to efficiently screen genome sequences for microsatellites (perfect as well as imperfect), we developed a new tool called IMEx (Imperfect Microsatellite Extractor). IMEx uses simple string-matching algorithm with sliding window approach to screen DNA sequences for microsatellites and reports the motif, copy number, genomic location, nearby genes, mutational events and many other features useful for in-depth studies. IMEx is more sensitive, efficient and useful than the available widely used tools. IMEx is available in the form of a stand-alone program as well as in the form of a web-server.