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RAPSearch2 is a tool for fast protein similarity searches. RAPSearch2 searches short DNA sequences (reads) or protein sequences against protein database, achieving >100 times speedup as compared to BLASTX (for reads of ~100bp), or >1000 times speedup over BLASTX in the accelerating mode (option "-a"). RAPSearch2 utilizes reduced amino acid alphabet and flexible seed so that seeds of various lengths with mismatches can be identified quickly by hashing.
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