Hybrid Gibbs-sampling algorithm for challenging motif discovery: GibbsDST.

Kazuhito Shida

研究成果: Article査読

3 被引用数 (Scopus)

抄録

The difficulties of computational discovery of transcription factor binding sites (TFBS) are well represented by (l, d) planted motif challenge problems. Large d problems are difficult, particularly for profile-based motif discovery algorithms. Their local search in the profile space is apparently incompatible with subtle motifs and large mutational distances between the motif occurrences. Herein, an improved profile-based method called GibbsDST is described and tested on (15,4), (12,3), and (18,6) challenging problems. For the first time for a profile-based method, its performance in motif challenge problems is comparable to that of Random Projection. It is noteworthy that GibbsDST outperforms a pattern-based algorithm, WINNOWER, in some cases. Effectiveness of GibbsDST using a biological dataset as an example and its possible extension to more realistic evolution models are also introduced.

本文言語English
ページ(範囲)3-13
ページ数11
ジャーナルGenome informatics. International Conference on Genome Informatics
17
2
出版ステータスPublished - 2006 1 1

ASJC Scopus subject areas

  • 医学(全般)

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