AMD, an Automated Motif Discovery Tool Using Stepwise Refinement of Gapped Consensuses

作者：Jiantao Shi, Wentao Yang, Mingjie Chen, Yanzhi Du, Ji Zhang, Kankan Wang · 发表于：PLoS ONE · 年份：2011 · DOI：10.1371/journal.pone.0024576 · 被引用次数：28 · 研究领域：Genomics and Chromatin Dynamics、Genomics and Phylogenetic Studies、Genetic Mapping and Diversity in Plants and Animals

Motif discovery is essential for deciphering regulatory codes from high throughput genomic data, such as those from ChIP-chip/seq experiments. However, there remains a lack of effective and efficient methods for the identification of long and gapped motifs in many relevant tools reported to date. We describe here an automated tool that allows for de novo discovery of transcription factor binding sites, regardless of whether the motifs are long or short, gapped or contiguous.