Dr.Fengzhu Sun:Alignment-Free Genome and...

  • wuyy@ucas.ac.cn
  • 创建时间: 2013-03-26

Dr.Fengzhu Sun,Molecular and Computational Biology Program, University of Southern California
Inviter: 生物信息中心 


Alignment-Free Genome and Metagenome Comparison Based on NGS Reads

Time & Venue: 
2013.3.27 10:00am S1013 


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. 

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.