PatSearch:: a program for the detection of patterns and structural motifs in nucleotide sequences
PatSearch:: a program for the detection of patterns and structural motifs in nucleotide sequences
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DOI：
10.1093/nar/gkg548
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发表时间：
2003-07-01
影响因子：
14.9
通讯作者：
Pesole, G
中科院分区：
文献类型：
--
作者：
Grillo, G;Licciulli, F;Pesole, G
基因表达在转录和转录后水平的调控涉及短的DNA或RNA片段与相应的反式作用蛋白质因子之间的相互作用。在全基因组筛选中检测这样的顺式作用元件可能显著有助于基因组注释和比较分析以及靶向功能表征实验。我们在这里提出PatSearch，一个灵活和快速的模式匹配器，能够搜索寡核苷酸的共识序列，二级结构元素和位置权重矩阵的特定组合。它还可以允许低于用户固定阈值的失配/错配。我们报告了三种不同的应用程序中的复杂模式，如铁响应元件发夹环结构，p53响应元件和启动子模块包含CAAT-，TATA-和帽盒的搜索。PatSearch可在http://bighost.area.ba.cnr.it/BIG/PatSearch/网站上找到。
Regulation of gene expression at transcriptional and post-transcriptional level involves the interaction between short DNA or RNA tracts and the corresponding trans-acting protein factors. Detection of such cis-acting elements in genome-wide screenings may significantly contribute to genome annotation and comparative analysis as well as to target functional characterization experiments. We present here PatSearch, a flexible and fast pattern matcher able to search for specific combinations of oligonucleotide consensus sequences, secondary structure elements and position-weight matrices. It can also allow for mismatches/mispairings below a user fixed threshold. We report three different applications of the program in the search of complex patterns such as those of the iron responsive element hairpin-loop structure, the p53 responsive element and a promoter module containing CAAT-, TATA- and cap-boxes. PatSearch is available on the web at http://bighost.area.ba.cnr.it/BIG/PatSearch/.