title: FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments.
abstract: CONCLUSIONS
  As was shown in Nagarajan et al. (2005), commonly used approximations for assessing the significance of multiple alignments can be be very inaccurate. To address this, we present here the FAST package, an open-source collection of programs and libraries for efficiently and reliably computing the significance of ungapped local alignments. We also describe other potential applications in Bioinformatics where these programs can be adapted for significance testing.
  
  
  BACKGROUND
  The FAST package includes C++ implementations of various algorithms that can be used as stand-alone programs or as a library of subroutines. The package and a web-server for some of the programs are available at www.cs.cornell.edu/~keich/FAST.
authors.affiliation: University of Maryland, College Park, MD 20740, USA.
authors.forename: Niranjan
authors.initials: N
authors.lastname: Nagarajan
authors.forename: Uri
authors.initials: U
authors.lastname: Keich
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D005583:Fourier Analysis; D016415:Sequence Alignment / Q000379:methods*