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RAPSearch: a fast protein similarity search tool for short reads

Yuzhen Ye1*, Jeong-Hyeon Choi2 and Haixu Tang12

Author Affiliations

1 School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA

2 Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA

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BMC Bioinformatics 2011, 12:159  doi:10.1186/1471-2105-12-159

Published: 15 May 2011



Next Generation Sequencing (NGS) is producing enormous corpuses of short DNA reads, affecting emerging fields like metagenomics. Protein similarity search--a key step to achieve annotation of protein-coding genes in these short reads, and identification of their biological functions--faces daunting challenges because of the very sizes of the short read datasets.


We developed a fast protein similarity search tool RAPSearch that utilizes a reduced amino acid alphabet and suffix array to detect seeds of flexible length. For short reads (translated in 6 frames) we tested, RAPSearch achieved ~20-90 times speedup as compared to BLASTX. RAPSearch missed only a small fraction (~1.3-3.2%) of BLASTX similarity hits, but it also discovered additional homologous proteins (~0.3-2.1%) that BLASTX missed. By contrast, BLAT, a tool that is even slightly faster than RAPSearch, had significant loss of sensitivity as compared to RAPSearch and BLAST.


RAPSearch is implemented as open-source software and is accessible at webcite. It enables faster protein similarity search. The application of RAPSearch in metageomics has also been demonstrated.

short reads; similarity search; suffix array; reduced amino acid alphabet; metagenomics