RAPSearch v2.09 (Fast protein similarity search tool for short reads that utilizes a reduced amino acid alphabet and suffix array to detect seeds of flexible length)
RAPSearch stands for Reduced Alphabet based Protein similarity Search. RAPSearch 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).
RAPSearch2 supports multiple threads
RAPSearch2works faster than RAPSearch and uses less memory