2008 Poster Sessions : DNA's Family Tree: Exploring the History of Extant Genomes

Student Name : Aaron Wenger
Advisor : Gill Bejerano
Research Areas: Artificial Intelligence
Abstract
DNA sequence alignment using BLAST and related algorithms enables the inference of shared origins and functional similarity. Of particular use are comparisons across species, which provide evidence for when in evolutionary time a sequence arose. The National Center for Biotechnology Information (NCBI) houses over 870 gigabases of sequence from more than 342,000 species, but it imposes strict CPU time constraints on searching the data. The constraints limit the depth, and hence utility, of searches. The BLASTZ Engine is a system that overcomes the constraints by maintaining a local mirror of the NCBI repository and efficiently executing searches on a local computer cluster.

Bio
Aaron Wenger is a graduate student in the Computer Science Ph.D. program at Stanford University. He received a B.S. in Computer Engineering, summa cum laude, from the University of Notre Dame in 2005. He is pursuing his interest in applying computational tools to biological problems in the lab of Gill Bejerano.