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

Vincent Ranwez

PLOS ONE, 2016, vol. 11, issue 8, 1-6

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.

Date: 2016
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0160043

DOI: 10.1371/journal.pone.0160043

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