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Two Simple and Efficient Algorithms to Compute the SP-Score Objective Function of a Multiple Sequence Alignment

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  • Vincent Ranwez

Abstract

Background: Multiple sequence alignment (MSA) is a crucial step in many molecular analyses and many MSA tools have been developed. Most of them use a greedy approach to construct a first alignment that is then refined by optimizing the sum of pair score (SP-score). The SP-score estimation is thus a bottleneck for most MSA tools since it is repeatedly required and is time consuming. Results: Given an alignment of n sequences and L sites, I introduce here optimized solutions reaching O(nL) time complexity for affine gap cost, instead of O(n2L), which are easy to implement.

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  • Vincent Ranwez, 2016. "Two Simple and Efficient Algorithms to Compute the SP-Score Objective Function of a Multiple Sequence Alignment," PLOS ONE, Public Library of Science, vol. 11(8), pages 1-6, August.
    • Handle: RePEc:plo:pone00:0160043
    DOI: 10.1371/journal.pone.0160043
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