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Fall 2008 CBMG Seminar (back to list)

September 19, 2008, 2 p.m.

Carl Kingsford
Center for Bioinformatics and Computational Biology,
University of Maryland, College Park

"Transcription Terminators, DNA uptake, and Overlapping Genes"

Abstract:

We discuss computational studies of several features of bacterial genomes.
In particular, we present TransTermHP, a program for finding Rho-independent
transcription terminators in genomic sequences. We construct a comprehensive
catalog of these terminators and their relationship to DNA uptake sequence
signals.  In the process, we discover a new variant of DNA uptake signal in
Haemophilus ducreyi.

Separately, we study the common phenomenon of overlapping bacterial genes.
We present a natural model based on the location of random stop codons that
largely explains both the observed distribution of overlap lengths and the
preference for certain intergenic distances between closely spaced,
non-overlapping genes.

Parts of this research were conducted in collaboration with Arthur Delcher,
Steven L. Salzberg, and Kunmi Ayanbule.

This seminar will be held at noon in Rm. 1103 Biosciences Research Building

Past seminars: Fall 2004 Spring 2005 Fall 2005 Spring 2006 Fall 2006 Spring 2007 Fall 2007 Spring 2008