SEPP and TIPP: New Phylogenetic Placement and Taxon Identification Methods for Metagenomic Data
Speaker: Tandy Warnow , University of Texas Austin
Date: May 16 2012
Time: 11:30AM to 1:00PM
Location: Stata Center 32-G575
Host: Bonnie Berger, MIT
Contact: Patrice Macaluso, 617.253.3037, macaluso@csail.mit.edu
Phylogenetic placement arises in the analysis of metagenomic data, in
which 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. 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 and Systematic Biology 2012, 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. Finally, we present TIPP, an extension of SEPP, that enables taxon identification for short reads, and which produces dramatically improved accuracy over current taxon identification methods.
Joint work with Siavash Mirarab and Nam Nguyen, PhD students at UT-Austin, and Bo Liu and Mihai Pop at the University of Maryland.
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