MSOAR 2.0 / MultiMSOAR 2.0
MSOAR may be used to perform ortholog assignment between two genomes A and B.(If two genomes have different number of chromosomes, it is required that A has more chromosomes than B).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.
MultiMSOAR is an acurrate identification of ortholog groups
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MSOAR 2.0: Incorporating Tandem Duplications into Ortholog Assignment Based on Genome Rearrangement
Guanqun Shi, Liqing Zhang, Tao Jiang,
In Proc. 8th LSS Computational Systems Bioinformatics Conference (CSB), Stanford, August, 2009, pp.12-24
MultiMSOAR 2.0: an accurate tool to identify ortholog groups among multiple genomes.
Shi G, Peng MC, Jiang T.
PLoS One. 2011;6(6):e20892. doi: 10.1371/journal.pone.0020892.