RAPSearch: a fast protein similarity search tool for short reads

Background: 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. Results: 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 similar to 20-90 times speedup as compared to BLASTX. RAPSearch missed only a small fraction (similar to 1.3-3.2%) of BLASTX similarity hits, but it also discovered additional homologous proteins (similar to 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. Conclusions: RAPSearch is implemented as open-source software and is accessible at http://omics.informatics.indiana.edu/mg/RAPSearch. It enables faster protein similarity search. The application of RAPSearch in metageomics has also been demonstrated.