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Nucleic Acids Research Advance Access originally published online on May 21, 2009
Nucleic Acids Research 2009 37(Web Server issue):W193-W201; doi:10.1093/nar/gkp388
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W193-W201
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

RegAnalyst: a web interface for the analysis of regulatory motifs, networks and pathways

Deepak Sharma*, Debasisa Mohanty and Avadhesha Surolia

National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India

*To whom correspondence should be addressed. Tel: +91 11 26703833; Fax: +91 11 26162125; Email: deepak{at}nii.res.in deepak.aiims{at}gmail.com

Received February 6, 2009. Revised April 18, 2009. Accepted April 29, 2009.

RegAnalyst is a user-friendly web interface that integrates MoPP (Motif Prediction Program), MyPatternFinder (pattern detection tool) and MycoRegDB (mycobacterial promoter and regulatory elements database). Since motif discovery is a challenging task, numerous tools have been developed over the past few years. Strikingly, the existing programs were not successful in detecting the known consensus in all mycobacterial (epitomizing degenerate) datasets even in the absence of noise and their performance was further reduced in the presence of noise. Consequently, MoPP, a de novo and greedy (for degeneracy) ‘inexact’ word-based tool that is tailored to enumerate significantly conserved degenerate oligonucleotide motifs was developed. Benchmarking on datasets from MycoRegDB and SCPD (http://rulai.cshl.edu/SCPD/) indicate that MoPP (i) consistently outperforms other motif discovery tools on highly degenerate as well as less degenerate datasets and (ii) successfully detects completely degenerate motifs (with no two instances of a pattern being exactly the same) even in the presence of noise. We have also developed another accessory program, MyPatternFinder, that scans a given sequence or genome to find exact or approximate matches to a query motif of any length identified by MoPP or any other user-defined motif. RegAnalyst will be a valuable tool for in silico analysis of regulatory networks and can be accessed at http://www.nii.ac.in/~deepak/RegAnalyst.


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