By Topic

Motif Search in DNA Sequences Using Generalized Suffix Tree

Sign In

Cookies must be enabled to login.After enabling cookies , please use refresh or reload or ctrl+f5 on the browser for the login options.

Formats Non-Member Member
$33 $13
Learn how you can qualify for the best price for this item!
Become an IEEE Member or Subscribe to
IEEE Xplore for exclusive pricing!
close button

puzzle piece

IEEE membership options for an individual and IEEE Xplore subscriptions for an organization offer the most affordable access to essential journal articles, conference papers, standards, eBooks, and eLearning courses.

Learn more about:

IEEE membership

IEEE Xplore subscriptions

3 Author(s)
Anjali Mohapatra ; SOAU, Bhubaneswar ; P. M. Mishra ; S. Padhy

There has been a growing interest in discovery of significant patterns in biological sequences that correspond to some structural and/ or functional feature of the bio-molecule known as motifs. It has important application in determining regulatory sites and drug target identification. Identification of motif is a challenging problem because motifs exist in different sequences in various mutated forms. In this paper, we consider the problem of finding the position of a given a motif of length I with up to d number of mismatches in a given set of DNA sequences. We represent the given set of sequences as a generalized suffix tree (GST) and obtain new data structures based on this tree. We develop a tree based algorithm to find motifs with allowable number of mismatches. Our algorithm aims to rank the search space, there by ensuring the highest ranking space contains the motif with allowable number of mismatches. Our hypothesis that the subtree under the highest ranking node is the most probable search space to contain the motif is explained through examples and implementation.

Published in:

Information Technology, (ICIT 2007). 10th International Conference on

Date of Conference:

17-20 Dec. 2007