May 31, 2016

RAFTS3: Rapid Alignment-Free Tool for Sequence Similarity Search

BioRxiv : the Preprint Server for Biology
Ricardo A VialleRoberto T Raittz

Abstract

Similarity search of a given protein sequence against a database is an essential task in genome analysis. Sequence alignment is the most used method to perform such analysis. Although this approach is efficient, the time required to perform searches against large databases is always a challenge. Alignment-free techniques offer alternatives to comparing sequences without the need of alignment. We developed RAFTS3, a fast protein similarity search tool that utilizes a filter step for candidate selection based on shared k-mers and a comparison measure using a binary matrix of co-occurrence of amino acid residues. RAFTS3 performed searches many times faster than those with BLASTp against large protein databases, such as NR, Pfam or UniRef, with a small loss of sensitivity depending on the similarity degree of the sequences. RAFTS3 is a new alternative for fast comparison of protein sequences, genome annotation and biological data mining. The source code and the standalone files for Windows and Linux platform are available at: https://sourceforge.net/projects/rafts3/

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