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Heuristic Alignment Methods

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Multiple Sequence Alignment Methods

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1079))

Abstract

Computation of multiple sequence alignment (MSA) is usually formulated as a combinatory optimization problem of an objective function. Solving the problem for virtually all sensible objective functions is known to be NP-complete implying that some heuristics must be adopted. Several general strategies have been proven effective to obtain accurate MSAs in reasonable computational costs. This chapter is devoted to a brief summary of most successful heuristic approaches.

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Acknowledgment

I thank Dr. Kentaro Tomii for instruction about protein fold recognition methods. This work was partly supported by Kakenhi (Grant-in-Aid for Scientific Research) B (grant number 22310124) from the Ministry of Education, Culture, Sports, Science and Technology of Japan.

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Authors and Affiliations

  1. Computational Biology Research Center (CBRC), Tokyo, Japan

    Osamu Gotoh

  2. National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan

    Osamu Gotoh

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  1. Osamu Gotoh
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  1. Dept. of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA

    David J Russell

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Gotoh, O. (2014). Heuristic Alignment Methods. In: Russell, D. (eds) Multiple Sequence Alignment Methods. Methods in Molecular Biology, vol 1079. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-646-7_2

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  • DOI: https://doi.org/10.1007/978-1-62703-646-7_2

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