PT  - JOURNAL ARTICLE
AU  - Ricardo Assunção Vialle
AU  - Fábio de Oliveira Pedrosa
AU  - Vinicius Almir Weiss
AU  - Dieval Guizelini
AU  - Juliana Helena Tibaes
AU  - Jeroniza Nunes Marchaukoski
AU  - Emanuel Maltempi de Souza
AU  - Roberto Tadeu Raittz
TI  - RAFTS3: Rapid Alignment-Free Tool for Sequence Similarity Search
AID  - 10.1101/055269
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 055269
4099  - http://biorxiv.org/content/early/2016/05/31/055269.short
4100  - http://biorxiv.org/content/early/2016/05/31/055269.full
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/