Finding motifs in the twilight zone.

@article{citeulike:878340, abstract = {MOTIVATION: Gene activity is often affected by binding transcription factors to short fragments in DNA sequences called motifs. Identification of subtle regulatory motifs in a DNA sequence is a difficult pattern recognition problem. In this paper we design a new motif finding algorithm that can detect very subtle motifs. RESULTS: We introduce the notion of a multiprofile and use it for finding subtle motifs in DNA sequences. Multiprofiles generalize the notion of a profile and allow one to detect subtle patterns that escape detection by the standard profiles. Our MULTIPROFILER algorithm outperforms other leading motif finding algorithms in a number of synthetic models. Moreover, it can be shown that in some previously studied motif models, MULTIPROFILER is capable of pushing the performance envelope to its theoretical limits. AVAILABILITY: http://www-cse.ucsd.edu/groups/bioinformatics/software.html}, address = {Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA. keich@cs.ucsd.edu}, author = {Keich, U. and Pevzner, P. A. }, citeulike-article-id = {878340}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {gene-activity}, month = {October}, number = {10}, pages = {1374--1381}, posted-at = {2008-01-21 23:01:26}, priority = {2}, title = {Finding motifs in the twilight zone.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/12376382}, volume = {18}, year = {2002} }

TY - JOUR ID - citeulike:878340 L3 - citeulike-article-id:878340 N2 - MOTIVATION: Gene activity is often affected by binding transcription factors to short fragments in DNA sequences called motifs. Identification of subtle regulatory motifs in a DNA sequence is a difficult pattern recognition problem. In this paper we design a new motif finding algorithm that can detect very subtle motifs. RESULTS: We introduce the notion of a multiprofile and use it for finding subtle motifs in DNA sequences. Multiprofiles generalize the notion of a profile and allow one to detect subtle patterns that escape detection by the standard profiles. Our MULTIPROFILER algorithm outperforms other leading motif finding algorithms in a number of synthetic models. Moreover, it can be shown that in some previously studied motif models, MULTIPROFILER is capable of pushing the performance envelope to its theoretical limits. AVAILABILITY: http://www-cse.ucsd.edu/groups/bioinformatics/software.html IS - 10 JF - Bioinformatics SN - 1367-4803 AD - Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA. keich@cs.ucsd.edu EP - 1381 TI - Finding motifs in the twilight zone. VL - 18 SP - 1374 KW - gene-activity AU - Keich, U AU - Pevzner, PA PY - 2002/10// UR - http://view.ncbi.nlm.nih.gov/pubmed/12376382 ER -