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Towards Construction of Optimal Strip-Exchanging Moves

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2 Author(s)
Swapnoneel Roy ; IBM India Pvt. Ltd., swapnoneel.roy@in.ibm.com ; Ashok Kumar Thakur

Genome and other syntenic blocks rearrangements have become a topic of intensive study by phylogenists, comparative genomicists, and computational biologists: they are a feature of many cancers, must be taken into account to align highly divergent sequences, and constitute a phylogenetic marker of great interest. The mathematics of rearrangements is far more complex than for indels and mutations in sequences. Genome rearrangements have been modeled by a variety of primitives such as reversals, transpositions , block moves and block interchanges. In this paper, we study a genome rearrangement primitive called strip exchanges. We formulate the primitive as a special case of another primitive, the block interchanges, identify a new lower bound for the sorting by strip exchanges problem. We then design a 2 approximation algorithm for the problem.

Published in:

2007 IEEE 7th International Symposium on BioInformatics and BioEngineering

Date of Conference:

14-17 Oct. 2007