Please use this identifier to cite or link to this item:
Title: Localized motif discovery in gene regulatory sequences
Authors: Narang, V.
Mittal, A.
Sung, W.-K. 
Issue Date: 2010
Citation: Narang, V., Mittal, A., Sung, W.-K. (2010). Localized motif discovery in gene regulatory sequences. Bioinformatics 26 (9) : 1152-1159. ScholarBank@NUS Repository.
Abstract: Motivation: Discovery of nucleotide motifs that are localized with respect to a certain biological landmark is important in several applications, such as in regulatory sequences flanking the transcription start site, in the neighborhood of known transcription factor binding sites, and in transcription factor binding regions discovered by massively parallel sequencing (ChIP-Seq). Results: We report an algorithm called LocalMotif to discover such localized motifs. The algorithm is based on a novel scoring function, called spatial confinement score, which can determine the exact interval of localization of a motif. This score is combined with other existing scoring measures including over-representation and relative entropy to determine the overall prominence of the motif. The approach successfully discovers biologically relevant motifs and their intervals of localization in scenarios where the motifs cannot be discovered by general motif finding tools. It is especially useful for discovering multiple co-localized motifs in a set of regulatory sequences, such as those identified by ChIP-Seq. Availability and Implementation: The LocalMotif software is available at Contact: Supplementary information: Supplementary data are available at Bioinformatics online. © The Author 2010. Published by Oxford University Press. All rights reserved. For Permissions, please email:
Source Title: Bioinformatics
ISSN: 13674803
DOI: 10.1093/bioinformatics/btq106
Appears in Collections:Staff Publications

Show full item record
Files in This Item:
There are no files associated with this item.


checked on Oct 17, 2018


checked on Oct 9, 2018

Page view(s)

checked on Sep 29, 2018

Google ScholarTM



Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.