title: A random-permutations-based approach to fast read alignment.
abstract: BACKGROUND
  Read alignment is a computational bottleneck in some sequencing projects. Most of the existing software packages for read alignment are based on two algorithmic approaches: prefix-trees and hash-tables. We propose a new approach to read alignment using random permutations of strings.
  
  
  RESULTS
  We present a prototype implementation and experiments performed with simulated and real reads of human DNA. Our experiments indicate that this permutations-based prototype is several times faster than comparable programs for fast read alignment and that it aligns more reads correctly.
  
  
  CONCLUSIONS
  This approach may lead to improved speed, sensitivity, and accuracy in read alignment. The algorithm can also be used for specialized alignment applications and it can be extended to other related problems, such as assembly.More information: http://alignment.commons.yale.edu.
authors.affiliation: Applied Mathematics Program, Yale University, 51 Prospect St., New Haven, CT 06511, USA. roy.lederman@yale.edu
authors.forename: Roy
authors.initials: R
authors.lastname: Lederman
mesh_terms: D000465:Algorithms; D006801:Humans; D054643:INDEL Mutation; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA; D012984:Software