CS 201: SEPP: SATe-enabled phylogenetic placement, TANDY WARNOW, University of Texas at Austin
Nov 03, 2011
from 04:15 PM to 05:45 PM
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|Contact Phone||310 825-4033|
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SEPP: SATe-enabled phylogenetic placement
Professor Tandy Warnow
University of Texas at Austin
Phylogenetic placement arises in the analysis of metagenomic data, inwhich the objective is to insert short molecular sequences (called "query sequences") into an existing phylogenetic tree and alignment on full-length sequences for the same gene. Phylogenetic placement has the potential to provide information beyond pure species identification (i.e, the association of metagenomic reads to existing species), because it can also give information about the evolutionary relationships between these query sequences and to known species. We present SEPP, a general "boosting" technique to improve the accuracy and/or speed of phylogenetic placement techniques. The key algorithmic aspect of SEPP is a dataset decomposition technique in SATe (Liu et al., Science 2009), a method that utilizes an iterative divide-and-conquer technique to co-estimate alignments and trees on large molecular sequence datasets. We show that SEPP improves current phylogenetic placement methods, placing metagenomic sequences more accurately when the set of input sequences has a large evolutionary diameter and produces placements of comparable accuracy in a fraction of the time for easier cases.
Joint work with Siavash Mirarab and Nam Nguyen, PhD students at UT-Austin.
Tandy Warnow is the David Bruton, Jr. Centennial Professor in Computer Science at the University of Texas at Austin. She received her PhD in Mathematics at UC Berkeley in 1991 under the supervision of Gene Lawler, and was a postdoc with Simon Tavare and Mike Waterman at USC from 1991-1992. Her research focuses on the development of mathematical models and algorithms for estimating evolutionary history in Biology and Historical Linguistics. Her research is currently funded by the National Science Foundation and the John Simon Guggenheim Foundation. She has also been awarded a David and Lucile Packard Foundation Fellowship, a Radcliffe Institute for Advanced Study Fellowship, and the NSF Young Investigator Award. She currently chairs the BDMA study section at NIH.
Hosted by Prof Sebastien Roch
DATE: Thursday, November 3, 2011
** Refreshments at 4:00pm, Speaker at 4:15pm **
TIME: 4:15 – 5:45 P.M.
PLACE: 3400 Boelter Hall