Institute of Information Science, Academia Sinica

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Seminar

Software and Algorithms for Next-gen sequencing and beyond

  • LecturerPaul Horton (Research Team Leader, AIST, Computational Biology Research Center)
    Host: Dr. Chung-Yen Lin
  • Time2010-02-26 (Fri.) 14:00 – 16:00
  • LocationAuditorium 106 at new IIS Building
Abstract
First, I will briefly introduce the computational biology program in the Graduate School of Frontier Science of the University of Tokyo where I have a visiting position. Then I will talk about software and algorithms related to next-gen sequencing being carried out in my group. LAST is an alignment program developed mainly by Martin Frith (it is essentially a much faster way to do what BLAST can do). DisLeX is a related algorithm developed by myself and Martin. RECOUNT is a software program developed mainly by Edward Wijaya and myself to reduce the affect of sequencing error on analysis of expression or metagenomic data. References "Incorporating sequence quality data into alignment improves DNA read mapping" Martin C. Frith; Raymond Wan; Paul Horton, Nucleic Acids Research 2010; doi: 10.1093/nar/gkq010 "Parameters for accurate genome alignment", In press, BMC Bioinformatics, 2010. "RECOUNT: Next Generation Sequencing Error Correction Tool", Edward Wijaya, Martin C. Frith, Yutaka Suzuki & Paul Horton, Proceedings of 20th International Conference on Genome Informatics (GIW2009), Tokyo, Japan, December 2009. "DisLex: a Transformation for Discontiguous Suffix Array Construction", Paul Horton, Szymon M. Kielbasa and Martin C. Frith, Proceedings of the workshop on Knowledge, Language, and Learning in Bioinformatics (KLLBI), Hanoi, Vietnam, pp. 1-11, December 2008.