Fast Algorithm for Extracting Multiple Unordered Short Motifs Using Bit Operations

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

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.

Original languageEnglish
Title of host publicationProceedings of the 6th Joint Conference on Information Sciences, JCIS 2002
EditorsJ.H. Caulfield, S.H. Chen, H.D. Cheng, R. Duro, J.H. Caufield, S.H. Chen, H.D. Cheng, R. Duro, V. Honavar
Pages1180-1185
Number of pages6
Publication statusPublished - 2002
EventProceedings of the 6th Joint Conference on Information Sciences, JCIS 2002 - Research Triange Park, NC, United States
Duration: Mar 8 2002Mar 13 2002

Publication series

NameProceedings of the Joint Conference on Information Sciences
Volume6

Other

OtherProceedings of the 6th Joint Conference on Information Sciences, JCIS 2002
Country/TerritoryUnited States
CityResearch Triange Park, NC
Period3/8/023/13/02

All Science Journal Classification (ASJC) codes

  • Computer Science(all)

Fingerprint

Dive into the research topics of 'Fast Algorithm for Extracting Multiple Unordered Short Motifs Using Bit Operations'. Together they form a unique fingerprint.

Cite this