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[Algorithms and Computational Biology Lab]


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  Introduction to a high-throughput ortholog assignment system (MSOAR)

The assignment of orthologous genes between a pair of genomes is usually done using sequence similarity search. We recently proposed an ortholog assignment program (SOAR for System for Ortholog Assignment by Reversals) based on a new combinatorial approach that combines sequence similarity and genome rearrangements. Here we continue the development of this approach and unite genome rearrangement events and (post-speciation) duplication events in a single framework under the parsimony principle. In this framework, homologous gene are identified using sequence similarity search and orthologous genes are assumed to correspond to each other in the most parsimonious evolutionary scenario involving both genome rearrangements and (post-speciation) gene duplications. Besides several original algorithmic contributions, the enhanced method allows for the detection of inparalogs (i.e. paralogs produced by post-speciation duplications). The approach has been implemented as a high-throughput system, called MSOAR, for genome-scale ortholog assignment. Our simulation real data experiments demonstrate that MSOAR works well for closely related genomes such as human and mouse.

  • Accurate Identification of Ortholog Groups among Multiple Genomes [Paper]
    Guanqun Shi, Meng-Chih Peng, Tao Jiang,
    In Proc. 9th LSS Computational Systems Bioinformatics Conference (CSB), Stanford, August, 2010, pp.166-179
  • MSOAR 2.0: Incorporating Tandem Duplications into Ortholog Assignment Based on Genome Rearrangement [Paper]
    Guanqun Shi, Liqing Zhang, Tao Jiang,
    In Proc. 8th LSS Computational Systems Bioinformatics Conference (CSB), Stanford, August, 2009, pp.12-24
  • Clustering of Main Orthologs for Multiple Genomes [Paper]
    Zheng Fu, Tao Jiang,
    Journal of Bioinformatics and Computational Biology (JBCB) 6(3): 573-84, 2008; An extended abstract of the paper has also appear in Proc. 6th LSS Computational Systems Bioinformatics Conference (CSB), San Diego 2007, pp.195-202.
  • MSOAR: A High-Throughput Ortholog Assignment System Based on Genome Rearrangement [Paper]
    Zheng Fu, Xin Chen, Vladimir Vacic, Peng Nan, Yang Zhong, and Tao Jiang,
    Journal of Computational Biology 14(9), pp. 1160-1175, 2007.
  • A parsimony approach to genome-wide ortholog assignment [Paper]
    Zheng Fu, Xin Chen, Vladimir Vacic, Peng Nan, Yang Zhong, and Tao Jiang,
    RECOMB 2006, LNBI3909, pp. 578-594, 2006.
  • Assignment of orthologous genes via genome rearrangement [Paper]
    Xin Chen, Jie Zheng, Zheng Fu, Peng Nan, Yang Zhong, Stefano Lonardi and Tao Jiang,
    IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Vol. 2 No. 4, pp. 302-315.

Copyright @ by MSOAR Group (zfu@cs.ucr.edu), 2006

Last Modified on 11/02/2006