RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

Bioinformatics. 2012 Jan 1;28(1):125-6. doi: 10.1093/bioinformatics/btr595. Epub 2011 Oct 28.


Summary: With the wide application of next-generation sequencing (NGS) techniques, fast tools for protein similarity search that scale well to large query datasets and large databases are highly desirable. In a previous work, we developed RAPSearch, an algorithm that achieved a ~20-90-fold speedup relative to BLAST while still achieving similar levels of sensitivity for short protein fragments derived from NGS data. RAPSearch, however, requires a substantial memory footprint to identify alignment seeds, due to its use of a suffix array data structure. Here we present RAPSearch2, a new memory-efficient implementation of the RAPSearch algorithm that uses a collision-free hash table to index a similarity search database. The utilization of an optimized data structure further speeds up the similarity search-another 2-3 times. We also implemented multi-threading in RAPSearch2, and the multi-thread modes achieve significant acceleration (e.g. 3.5X for 4-thread mode). RAPSearch2 requires up to 2G memory when running in single thread mode, or up to 3.5G memory when running in 4-thread mode.

Availability and implementation: Implemented in C++, the source code is freely available for download at the RAPSearch2 website: http://omics.informatics.indiana.edu/mg/RAPSearch2/.

Contact: yye@indiana.edu

Supplementary information: Available at the RAPSearch2 website.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms*
  • Databases, Protein*
  • Gene Expression Profiling
  • High-Throughput Nucleotide Sequencing*
  • Programming Languages
  • Proteins / chemistry
  • Proteins / genetics*
  • Search Engine*
  • Software


  • Proteins