An efficient parallel algorithm for multiple sequence similarities calculation using a low complexity method

Biomed Res Int. 2014;2014:563016. doi: 10.1155/2014/563016. Epub 2014 Jul 22.

Abstract

With the advance of genomic researches, the number of sequences involved in comparative methods has grown immensely. Among them, there are methods for similarities calculation, which are used by many bioinformatics applications. Due the huge amount of data, the union of low complexity methods with the use of parallel computing is becoming desirable. The k-mers counting is a very efficient method with good biological results. In this work, the development of a parallel algorithm for multiple sequence similarities calculation using the k-mers counting method is proposed. Tests show that the algorithm presents a very good scalability and a nearly linear speedup. For 14 nodes was obtained 12x speedup. This algorithm can be used in the parallelization of some multiple sequence alignment tools, such as MAFFT and MUSCLE.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Computational Biology / methods*
  • Genome
  • Sequence Alignment
  • Sequence Homology*
  • Software*