RAPSearch: a tool for fast protein similarity search

• News: We have released RAPSearch2, a version that supports multiple threads! (Go to RAPSearch2)
• RAPSearch stands for Reduced Alphabet based Protein similarity Search
• Introduction: RAPSearch 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).
• Citation
  Yuzhen Ye, Jeong-Hyeon Choi and Haixu Tang. RAPSearch: a Fast Protein Similarity Search Tool for Short Reads. BMC Bioinformatics 2011, 12:159. (paper at BMC Bioinformatics)
• Download the software (v1.02) (a readme file with simple instructions is included in the package)
  
  • New in the latest version (version 1.02):
    Fixed a bug so that query short nucleotide sequences will not be mistaken as protein sequences
  • Get the most recent readme file
  • All versions
• Sample input files: 4440037.3.dna.fa (a query file) and nogCOGdomN95.seq (a database of protein sequences); RAPSearch results
• More tests & results
• Contact: Yuzhen Ye (yye@indiana.edu) (web)

Last modified on April 20th, 2011