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).