An extension and novel solution to the (l,d)-motif challenge problem.

Authors

• Mark P Styczynski
• Kyle L Jensen
• Isidore Rigoutsos
• Gregory N Stephanopoulos

Publication/Presentation Date

1-1-2004

Abstract

The (l,d)-motif challenge problem, as introduced by Pevzner and Sze, is a mathematical abstraction of the DNA functional site discovery task. Here we expand the (l,d)-motif problem to more accurately model this task and present a novel algorithm to solve this extended problem. This algorithm is guaranteed to find all (l,d)-motifs in a set of input sequences with unbounded support and length. We demonstrate the performance of the algorithm on publicly available datasets and show that the algorithm deterministically enumerates the optimal motifs.

Volume

15

Issue

2

First Page

63

Last Page

71

ISSN

0919-9454

Published In/Presented At

Styczynski, M. P., Jensen, K. L., Rigoutsos, I., & Stephanopoulos, G. N. (2004). An extension and novel solution to the (l,d)-motif challenge problem. Genome informatics. International Conference on Genome Informatics, 15(2), 63–71.

Disciplines

Business Administration, Management, and Operations | Health and Medical Administration | Management Sciences and Quantitative Methods

PubMedID

15706492

Department(s)

Administration and Leadership

Document Type

Article