RT Journal Article
SR Electronic
T1 RAFTS3: Rapid Alignment-Free Tool for Sequence Similarity Search
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 055269
DO 10.1101/055269
A1 Ricardo Assunção Vialle
A1 Fábio de Oliveira Pedrosa
A1 Vinicius Almir Weiss
A1 Dieval Guizelini
A1 Juliana Helena Tibaes
A1 Jeroniza Nunes Marchaukoski
A1 Emanuel Maltempi de Souza
A1 Roberto Tadeu Raittz
YR 2016
UL http://biorxiv.org/content/early/2016/05/31/055269.abstract
AB Background 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.Results Here 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. RAFTS3performed 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.Conclusions RAFTS3 is a new alternative for fast comparison of proteinsequences 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/