Mrázek Jan
Department of Microbiology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602-2605, USA.
Brief Bioinform. 2009 Sep;10(5):525-36. doi: 10.1093/bib/bbp032. Epub 2009 Jun 24.
Finding significant nucleotide sequence motifs in prokaryotic genomes can be divided into three types of tasks: (1) supervised motif finding, where a sample of motif sequences is used to find other similar sequences in genomes; (2) unsupervised motif finding, which typically relates to the task of finding regulatory motifs and protein binding sites and (3) exploratory motif finding, which aims to identify potential functionally significant sequence motifs as those that are unusual in some statistical sense. This article provides a conceptual overview for each type of task, a brief description of basic algorithms used in their solution, and a review of selected relevant software available online.
（1）有监督的基序寻找，即使用基序序列样本在基因组中寻找其他相似序列；（2）无监督的基序寻找，通常涉及寻找调控基序和蛋白质结合位点的任务；（3）探索性基序寻找，旨在识别在某些统计意义上不寻常的、具有潜在功能重要性的序列基序。本文对每种任务类型进行了概念性概述，简要描述了用于解决这些任务的基本算法，并对一些在线可用的相关软件进行了综述。
