RAPSearch2: an even faster RAPSearch that supports multi-threading

• RAPSearch stands for Reduced Alphabet based Protein similarity Search (more on RAPSearch)
• What's improved in RAPSearch2
  • RAPSearch2 works faster than the original RAPSearch; uses less memory; and supports multi-threading!
• Download RAPSearh2 from SourceForge or GitHub
• Important notes:
  
  • be sure to set -z parameter if you want to use more than one thread.
    
  • if you are switching from RAPSearch to RAPSearch2, please make sure that you prepare a new index file for database search using prerapsearch that comes with the new RAPSearch2 package.
    
  • RAPSearch supposes that there is no '(' in the first split part of query id. Please remove it!
    
• Sample input files: 4440037.3.dna.fa (a query file) and nogCOGdomN95.seq (a database of protein sequences); RAPSearch2 results
• Contact: Yongan Zhao (yongzhao@indiana.edu) and Yuzhen Ye (yye@indiana.edu) (web)
• Citations
  Yongan Zhao, Haixu Tang and Yuzhen Ye. RAPSearch2: a fast and memory-efficient protein similarity search tool for next generation sequencing data. Bioinformatics 2012, 28 (1): 125-126
  Yuzhen Ye, Jeong-Hyeon Choi and Haixu Tang. RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinformatics 2011, 12:159
  

Last modified on June 28, 2014