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      Aligning 415 519 proteins in less than two hours on PC

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          Abstract

          Rapid development of modern sequencing platforms enabled an unprecedented growth of protein families databases. The abundance of sets composed of hundreds of thousands sequences is a great challenge for multiple sequence alignment algorithms. In the article we introduce FAMSA, a new progressive algorithm designed for fast and accurate alignment of thousands of protein sequences. Its features include the utilisation of longest common subsequence measure for determining pairwise similarities, a novel method of gap costs evaluation, and a new iterative refinement scheme. Importantly, its implementation is highly optimised and parallelised to make the most of modern computer platforms. Thanks to the above, quality indicators, namely sum-of-pairs and total-column scores, show FAMSA to be superior to competing algorithms like Clustal Omega or MAFFT for datasets exceeding a few thousand of sequences. The quality does not compromise time and memory requirements which are an order of magnitude lower than that of existing solutions. For example, a family of 415 519 sequences was analysed in less than two hours and required only 8GB of RAM. FAMSA is freely available at http://sun.aei.polsl.pl/REFRESH/famsa.

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          Author and article information

          Journal
          2016-03-22
          Article
          1603.06958

          http://arxiv.org/licenses/nonexclusive-distrib/1.0/

          Custom metadata
          q-bio.GN cs.DS

          Data structures & Algorithms, Genetics

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