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Bioinformatics Advance Access originally published online on January 6, 2008
Bioinformatics 2008 24(4):577-578; doi:10.1093/bioinformatics/btm594
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments

Niranjan Nagarajan 1,* and Uri Keich 2

1University of Maryland, College Park, MD-20740 and 2Cornell University, Ithaca, NY-14850, USA

*To whom correspondence should be addressed.


  Abstract

Summary: 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.

Availability: 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

Contact: keich{at}cs.cornell.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Alex Bateman

Received on September 10, 2007; revised on November 7, 2007; accepted on November 27, 2007

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