NUS School of Computing 
Postgraduate Seminar by

Mr. Vipin Narang

Title:
 
LocalMotif - An In-Silico Tool For Detecting Localized Motifs
in Regulatory Sequences
 
Date: 30 November 2006 at 2pm

Venue: Executive Classroom, SOC1, Level 5

Abstract:
 
In silico motif finding algorithms are often used for discovering
protein-DNA binding sites in a set of regulatory sequences.
Current algorithms mainly address motif discovery in short sequences. 
Analyzing long sequences can be quite challenging not only due
to increasing time and memory requirements of the algorithm, 
but also decreasing accuracy. However, in case the motif is localized
in a short interval of the long sequences relative to an anchor point,
it is tenable to detect it easily by restricting the search to that
interval. But the region of localization of the motif is not known
a priori. This paper reports an algorithm called LocalMotif to detect
localized motifs in long regulatory sequences. A novel score function
predicts the region of localization of the motif. This score is 
combined with other scoring measures including Z-score and relative
entropy to detect the motif. The algorithm is optimized for fast
processing of long regulatory sequences. Tests on simulated and real
datasets confirm that LocalMotif accurately determines the region of
localization of motifs and automatically discovers the biologically
relevant motifs, which can be detected by other motif finding 
algorithms only when the search is restricted to the relevant interval.
 

CV:
 
Vipin Narang is currently pursuing his Ph.D. in Computer Science
at NUS supervised by Dr. Wing-Kin Sung.  He received his B.Tech. (2000)
and M.S.Research (2002) both in Electrical Engineering from Indian
Institute of Technology, New Delhi.  His research interests include
 Bayesian networks, stochastic models, machine learning and gene regulation.