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

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 effi-ciently and reliably computing the significance of ungapped local alignments. We also describe other potential applications in Bioinfor-matics where these programs can be adapted for significance testing. Availability: The FAST package includes Cþþ 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