title: Two Simple and Efficient Algorithms to Compute the SP-Score Objective Function of a Multiple Sequence Alignment.
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.
authors: Montpellier SupAgro, UMR AGAP, 34060, Montpellier, France.
authors: Vincent
authors: V
authors: Ranwez
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D016415:Sequence Alignment