FAMSA: Fast and accurate multiple sequence alignment of huge protein families.

ABSTRACT: Rapid development of modern sequencing platforms has contributed to the unprecedented growth of protein families databases. The abundance of sets containing hundreds of thousands of sequences is a formidable challenge for multiple sequence alignment algorithms. The article introduces FAMSA, a new progressive algorithm designed for fast and accurate alignment of thousands of protein sequences. Its features include the utilization of the longest common subsequence measure for determining pairwise similarities, a novel method of evaluating gap costs, and a new iterative refinement scheme. What matters is that its implementation is highly optimized and parallelized to make the most of modern computer platforms. Thanks to the above, quality indicators, i.e. sum-of-pairs and total-column scores,

SUBMITTER: Deorowicz S 

PROVIDER: S-EPMC5037421 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature