Michael Mwangi's Rockefeller University Homepage
Overview
I am a Ph.D. student of
Eric D. Siggia
, who is a full professor in the
Center for Studies in Physics and Biology
at
Rockefeller University
and an adjunct professor in the
Physics Department
at
Cornell University.
Professor Siggia's research involves applications of statistical physics and
dynamical systems to cellular biophysics and bioinformatics. Below, I describe
some of our projects.
Projects
Genome wide identification of regulatory motifs in a single prokaryote.
Reference
To be announced
Synopsis
Since the DNA binding domain of a transcritpion factor complex usually consists
of two extended subunits that clamp onto the DNA double helix like a pair of tweezers, a
transcription factor in a prokaryote tends to recognize and bind to patterns in the primary DNA
sequence called dimers that each consist of specific left and right words seperated
by a fixed number of unspecific bases. By searching in operons' regulatory regions
for improbably infrequent dimers, one therefore may be able to identify regulatory
sites. First, we group the genes in a prokaryotic genome into operons using
various spacing and name criteria. After removing exact repeats (e.g. LTR's),
we search in the regulatory regions of our predicted operons for statistcally
over-represented dimers with words of A, C, G, and T. We then group the
over-represented dimers into clusters using our WLC algorithm. The
dimers in each cluster can reasonably be considered to be recognized and
bound to by a single transcription factor. Finally, using a weight or
interaction energy matrix approach, we use the resulting clusters of dimers to
predict regulatory sites.
Results
The final
results
obtained by applying our algorithm to a variety of prokaryotic genomes listed in GenBank
are encouraging.
Michael Mwangi
mwangi@morel.rockefeller.edu
Last revised: April, 2003