title: RAPSearch: a fast protein similarity search tool for short reads.
abstract: 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 ~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.
  
  
  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.
authors.affiliation: School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA. yye@indiana.edu
authors.forename: Yuzhen
authors.initials: Y
authors.lastname: Ye
authors.forename: Jeong-Hyeon
authors.initials: JH
authors.lastname: Choi
authors.forename: Haixu
authors.initials: H
authors.lastname: Tang
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D056186:Metagenomics; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*; D057386:Search Engine; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins