A tool for multiple sequence alignment.

Abstract

Multiple sequence alignment can be a useful technique for studying molecular evolution and analyzing sequence-structure relationships. Until recently, it has been impractical to apply dynamic programming, the most widely accepted method for producing pairwise alignments, to comparisons of more than three sequences. We describe the design and application of a tool for multiple alignment of amino acid sequences that implements a new algorithm that greatly reduces the computational demands of dynamic programming. This tool is able to align in reasonable time as many as eight sequences the length of an average protein.

Swarm Intelligence Algorithms in Bioinformatics

“…To evaluate the quality of an alignment, a popular choice is to use the SP (sum of pairs) score method [65]. The SP score basically sums the substitution scores of all possible pair-wise combinations of sequence characters in one column of a multiple sequence alignment.…”

Multiple Sequence Alignment by Ant Colony Optimization and Divide-and-Conquer

“…The characters in S n will have higher probability to be selected if it has higher pheromone on the logical edge connecting with S k [l], higher matching score with S k [l], and less deviation to mid(n). (2) After each ant completes a solution, the pheromone on its logical edges should be updated according the fitness of the solution. Let evap1 be the evaporation coefficient, 0≤evap1≤1, the value of phe(k,l,n,m) is updated according to formula (3).…”

Two applications of the divide&conquer principle in the molecular sciences

“…The recursion stops when a certain stopping criterion is fulfilled. The remaining subsequence families are then aligned by MSA [24], [18), and the resulting alignments are concatenated.…”