Center for Bioinformatics at KU

As part of our public Seminar Series
http://bioinformatics.ku.edu/seminars

May 1, Fri 2009
11:00 am, MRB 200 Conference Room

Stephen O. Opiyo

School of Biological Sciences, University of Nebraska-Lincoln, Nebraska

Mining G-protein coupled receptors from plant genomes

The human genome includes 800 or more G-protein coupled receptors (GPCRs), 557 are found in chicken, about 300 are found in the Drosophila melanogaster genome, and more than 1000 are found in the Caenorhabditis elegans genome. Compared to the numbers found in other organisms, only 22 GPCRs are found in Arabidopsis genome, and 15 are found in rice genome. It may be possible that plants do not require as many GPCRs as animals. However, it is also possible that alignment-based methods used to identify these proteins, e.g., profile hidden Markov models and PSI-BLAST can not identify some GPCRs from plants due to their low sequence similarities. In this talk, I will present how alignment-free methods were used to mine G-protein receptors from plant genomes.