RAPSearch (Reduced Alphabet based Protein similarity Search) is a tool for fast protein similarity search for short reads. RAPSearch utilizes reduced amino acid alphabet and flexible seed so that seeds of various lengths with mismatches can be identified quickly by using suffix array. For short reads (e.g., ~100 nts) we have tested, RAPSearch achieved ~50 times speedup as compared to BLAST (~100 times speedup as compared to BLAST+) at the cost of a small loss of similarity detection sensitivity (Evalue cutoff=1e-3).
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Yongan Zhao, Haixu Tang and Yuzhen Ye.
RAPSearch2: a fast and memory-efficient protein similarity search tool for next generation sequencing data.
Bioinformatics 2012, 28 (1): 125-126
Ye Y., et al.
RAPSearch: a fast protein similarity search tool for short reads.
BMC Bioinformatics 2011;12:159.