Date: Wednesday, 14 November 2007, 6:30 PM
Location: SAP LABS, Building D, 3410 Hillview Avenue,
Palo Alto, CA (Google
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Cost: Free and open to all who wish to attend, but membership is
only $10/year.
Topic
The availability of entire genome sequences has prompted researchers in bioinformatics to use genomes as universal coordinate systems for mapping various types of sequence information. In turn, bioinformatics researchers need computer programs that can efficiently and accurately map and align nucleotide and protein sequences to entire genomes. The problem of mapping and aligning cDNA sequences to genomes for the same species has essentially been solved, with programs such as GMAP. The remaining issues in the field are the ability to handle cross-species alignments and protein sequences.
Cross-species alignments enable us to leverage our knowledge about one species onto another. Mapping and alignment of protein sequences has certain advantages over nucleotide sequences, especially in cross-species comparisons, because protein sequences are evolutionarily more conserved than nucleotide sequences. In this talk, I will discuss our recent work in extending the algorithmic ideas of GMAP to handle cross-species and protein sequences.
About the Speaker
Thomas
Wu received his B.S. and M.S. from Stanford in 1984, his
M.D. from Harvard Medical School in 1992, and his Ph.D. in Computer Science
from MIT in 1992. He completed his internship and residency in Internal Medicine
at Stanford in 1994. He was a Postdoctoral Fellow in the Department of Biochemistry
at Stanford from 1994 to 1999. Since 1999, Dr. Wu has been a Senior Scientist
in the Department of Bioinformatics at Genentech.