PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance
PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance
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DOI：
10.1093/bioinformatics/16.5.439
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发表时间：
2000-05-01
期刊：
影响因子：
5.8
通讯作者：
D'Souza, M
中科院分区：
文献类型：
--
作者：
Pesole, G;Liuni, S;D'Souza, M
动机：识别与基因调控和表达有关的序列模式是分子生物学中的一个主要挑战。本文描述了一种新的算法和软件，用于搜索复杂的核苷酸和蛋白质序列，包括潜在的二级结构元素，并允许错配/错配对低于用户固定的阈值，并通过马尔可夫链模拟评估其出现的统计意义。结果：应用所提出的算法，通过搜索方法的敏感性和选择性，可以识别位于转录后调控基因的mRNA非翻译区的一些功能元件，如铁反应元件、组蛋白茎环结构和Selencysteine插入序列。
Motivation: The identification of sequence patterns involved in gene regulation and expression is a major challenge in molecular biology. In this paper we describe a novel algorithm and the software for searching nucleotide and protein sequences for complex nucleotide patterns including potential secondary structure Elements, also allowing for mismatches/mispairings below a user fixed threshold, and assessing the statistical significance of their occurrence through a Markov chain simulation.Results: The application of the proposed algorithm allowed the identification of some functional elements, such as the Iron Responsive Element, the Histone stem-loop structure and the Selenocysteine Insertion Sequence, located in the mRNA untranslated regions of post-transcriptionally regulated genes with the assessment of sensitivity and selectivity of the searching method.