Kalign-LCS - A More Accurate and Faster Variant of Kalign2 Algorithm for the Multiple Sequence Alignment Problem

Determination of similarities between species is a crucial issue in life sciences. This task is usually done by comparing fragments of genomic or proteomic sequences of organisms subjected to analysis. The basic procedure which facilitates these comparisons is called multiple sequence alignment. There are a lot of algorithms aiming at this problem, which are either accurate or fast. We present Kalign-LCS, a variant of fast Kalign2 algorithm, that addresses the accuracy vs. speed trade-off. It employs the longest common subsequence measure and was thoroughly optimized. Experiments show that it is faster than Kalign2 and produces noticeably more accurate alignments.