Title :
Message-passing for motif finding
Author :
Lee, Sang Hyun ; Vikalo, Haris ; Vishwanath, Sriram
Author_Institution :
Dept. of ECE, Univ. of Texas at Austin, Austin, TX, USA
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.
Keywords :
DNA; biology computing; genetics; graph theory; inference mechanisms; message passing; molecular biophysics; optimisation; DNA sequence; computationally intensive combinatorial optimization; efficient heuristic algorithm; gene expression analysis; graph-based inference study; graphical message-passing model; graphical representation; message-passing algorithm; motif finding analysis; Biology computing; Computational biology; DNA; Gene expression; Genomics; Graphical models; Inference algorithms; Physics; Probability; Sequences;
Conference_Titel :
Genomic Signal Processing and Statistics, 2009. GENSIPS 2009. IEEE International Workshop on
Conference_Location :
Minneapolis, MN
Print_ISBN :
978-1-4244-4761-9
Electronic_ISBN :
978-1-4244-4762-6
DOI :
10.1109/GENSIPS.2009.5174332
