Fast Algorithm for Extracting Multiple Unordered Short Motifs Using Bit Operations

Osamu Maruyama, Hideo Bannai, Yoshinori Tamada, Satoru Kuhara, Satoru Miyano

研究成果: Chapter in Book/Report/Conference proceedingConference contribution

抄録

In this paper, we consider the problem of extracting multiple unordered short motifs in upstream regions of given genes. Multiple unordered short motifs can be considered as a set of short motifs, say M = {m 1, m 2,...,m k}. For a gene g, if each of the motifs m 1,...,m k occurs in either the upstream region or its complement of g, the gene g is said to be consistent with M. We have developed a fast method to exhaustively search collections of short motifs over given short motifs for a particular set of genes, and rank collections with using multiple objective functions. This method is implemented by employing bit operations in the process of matching short motifs with upstream regions, and identifying the members of genes which are consistent with short motifs. On various putatively co-regulated genes of S. cerevisiae, determined by gene expression profiles, our computational experiments show biologically interesting results.

本文言語英語
ホスト出版物のタイトルProceedings of the 6th Joint Conference on Information Sciences, JCIS 2002
編集者J.H. Caulfield, S.H. Chen, H.D. Cheng, R. Duro, J.H. Caufield, S.H. Chen, H.D. Cheng, R. Duro, V. Honavar
ページ1180-1185
ページ数6
出版ステータス出版済み - 2002
イベントProceedings of the 6th Joint Conference on Information Sciences, JCIS 2002 - Research Triange Park, NC, 米国
継続期間: 3 8 20023 13 2002

出版物シリーズ

名前Proceedings of the Joint Conference on Information Sciences
6

その他

その他Proceedings of the 6th Joint Conference on Information Sciences, JCIS 2002
国/地域米国
CityResearch Triange Park, NC
Period3/8/023/13/02

All Science Journal Classification (ASJC) codes

  • コンピュータ サイエンス(全般)

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