Skip Navigation



Bioinformatics Advance Access published online on May 5, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm118
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary data
Right arrow All Versions of this Article:
23/12/1476    most recent
btm118v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Wijaya, E.
Right arrow Articles by Sung, W.-K.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Wijaya, E.
Right arrow Articles by Sung, W.-K.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Detection of generic spaced motifs using submotif pattern mining

Edward Wijaya a,b, Rajaraman Kanagasabai a, Siu-Ming Yiu d and Wing-Kin Sung b,c,*

aInstitute for Infocomm Research , 21 Heng Mui Keng Terrace , Singapore 119613.
bSchool of Computing , National University of Singapore , Singapore 119260.
cGenome Institute of Singapore , 60 Biopolis Street , #02-01 Genome , Singapore 138672.
dDepartment of Computer Science, The University of Hong Kong, Pokfulam Road, Hong Kong.

*To whom correspondence should be addressed. Wing-Kin Sung, E-mail: ksung{at}comp.nus.edu.sg


  Abstract

Motivation: Identification of motifs is one of the critical stages in studying the regulatory interactions of genes. Motifs can have complicated patterns. In particular, spaced motifs, an important class of motifs, consist of several short segments separated by spacers of different lengths. Locating spaced motifs is not trivial. Existing motif-finding algorithms are either designed for monad motifs (short contiguous patterns with some mismatches) or have assumptions on the spacer lengths or can only handle at most two segments. An effective motif finder for generic spaced motifs is highly desirable.

Results: This paper proposes a novel approach for identifying spaced motifs with any number of spacers of different lengths. We introduce the notion of submotifs to capture the segments in the spaced motif and formulate the motif finding problem as a frequent submotif mining problem. We provide an algorithm called SPACE to solve the problem. Based on experiments on real biological datasets, synthetic datasets and the motif assessment benchmarks by Tompa et al., we show that our algorithm performs better than existing tools for spaced motifs with improvements in both sensitivity and specificity and for monads, SPACE performs as good as other tools.

Availability: The source code is available upon request from the authors.

Associate Editor: Prof. John Quackenbush

Received on December 5, 2006; revised on March 16, 2007; accepted on March 16, 2007

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
E. Wijaya, S.-M. Yiu, N. T. Son, R. Kanagasabai, and W.-K. Sung
MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders
Bioinformatics, October 15, 2008; 24(20): 2288 - 2295.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
C.-Y. Chen, H.-K. Tsai, C.-M. Hsu, M.-J. May Chen, H.-G. Hung, G. T.-W. Huang, and W.-H. Li
Discovering gapped binding sites of yeast transcription factors
PNAS, February 19, 2008; 105(7): 2527 - 2532.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.