William R. Pearson, PhD
Computational algorithms for analyzing genome and protein sequence data
The Pearson group develops computer programs for exploiting protein and DNA sequence information. They developed the FASTP and FASTA programs about 20 years ago; since then the program has been extensively improved to provide more sensitive and accurate protein and DNA searches. These improvements allow cancer researchers, and others, to identify homologous proteins from very distant relationships; the identification of distant homologs is routinely used to provide critical functional insights to poorly characterized proteins involved in oncogenesis.
Additions to the program package provide dramatically improved sensitivity for searching with short peptide sequences, such as those identified by MS/MS protein sequencing. The Pearson group has collaborated with Dr. Theodorescu, helping him identify proteins expressed in prostate cancer lines under different conditions.