Speaker

　　Fengzhu Sun, PhD, Molecular and Computational Biology Program, University of Southern California

　　Title

　  Alignment-Free Genome and Metagenome Comparison Based on NGS Reads

　　Time

　　2013.3.27 10:00-11:00am         

　　Venue

　　S1013

　　Abstract

    Next generation sequencing (NGS) technologieshave generated enormous
amount ofshotgun read data and assembly of the reads can be challenging,
especially fororganisms without template sequences. We develop novel alignment-free and assemble-free statistics for genome and metagenome comparison and study their limit behaviors. The statistics were used to study the evolutionary relationships among 13 tree species whose templates sequences are not known. They were also used to classify metagenomes from mammalian species, global ocean survey, and human gut.
In both applications, our novel statistics yield clustering that is consistent with biological knowledge. Thus, our statistics provide a powerful alternative approach for genome and metagenome comparison based on NGS short reads.

　　Affiliation

   B Jiang et al. (2012) Comparison of metagenomic samples using sequence signatures. BMC genomics 13 (1), 730
   K Song et al. (2012) Alignment-free sequence comparison based on next generation sequencing reads. Research in Computational Molecular Biology, 272-285