Message-passing for motif finding

Sang Hyun Lee, Haris Vikalo, Sriram Vishwanath

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

1 Citation (Scopus)

Abstract

A message-passing algorithm for motif finding is presented. Motif finding stands for the problem of identifying a collection of common subsequences within a given set of DNA sequences. Using a combinatorial framework for this problem, this paper describes it in terms of a graphical model. Subsequently, an inference problem is formulated over this graphical representation for the motif finding problem. The paper develops a message-passing algorithm to efficiently solve this graph-based inference problem. This algorithm serves as an efficient heuristic for solving what is otherwise a computationally intensive combinatorial optimization problem.

Original languageEnglish
Title of host publication2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009
DOIs
Publication statusPublished - 2009 Oct 2
Externally publishedYes
Event2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009 - Minneapolis, MN, United States
Duration: 2009 May 172009 May 21

Publication series

Name2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009

Conference

Conference2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009
CountryUnited States
CityMinneapolis, MN
Period09/5/1709/5/21

Fingerprint

Message passing
DNA sequences
Combinatorial optimization

ASJC Scopus subject areas

  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Vision and Pattern Recognition
  • Biomedical Engineering

Cite this

Lee, S. H., Vikalo, H., & Vishwanath, S. (2009). Message-passing for motif finding. In 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009 [5174332] (2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009). https://doi.org/10.1109/GENSIPS.2009.5174332

Message-passing for motif finding. / Lee, Sang Hyun; Vikalo, Haris; Vishwanath, Sriram.

2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009. 2009. 5174332 (2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009).

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

Lee, SH, Vikalo, H & Vishwanath, S 2009, Message-passing for motif finding. in 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009., 5174332, 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009, 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009, Minneapolis, MN, United States, 09/5/17. https://doi.org/10.1109/GENSIPS.2009.5174332
Lee SH, Vikalo H, Vishwanath S. Message-passing for motif finding. In 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009. 2009. 5174332. (2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009). https://doi.org/10.1109/GENSIPS.2009.5174332
Lee, Sang Hyun ; Vikalo, Haris ; Vishwanath, Sriram. / Message-passing for motif finding. 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009. 2009. (2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS 2009).
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