View source for FAST Alignment and Search Tool

'''FAST Alignment and Search Tool''' (or, just '''FAST''') is a new algorithm for aligning three-dimensional structures of proteins.<ref name=Zhu2005>Zhu J, Weng Z (2005). FAST: a novel protein structure alignment algorithm. ''Proteins: Structure, Function and Bioinformatics (14):417-423''.</ref> FAST employs an elimination heuristic to quickly and reliably detect the global optimum residue-residue alignment. The main application is detection of structural and functional similarities that are not available with traditional sequence alignment algorithms. FAST can be [http://biowulf.bu.edu/FAST/index.htm run from the web] by uploading two PDB files in the given form. Or, one can also [http://biowulf.bu.edu/FAST/download.htm download the executable] for off-line use.

FAST is developed by Jianhua Zhu at the Bioinformatics Program of Boston University.

==Usage==
 % fast protein1 protein2 [-r rasmol-script]
 
 %1              fn      protein #1
 %2              fn      protein #2
 -o|--out        fn      output file name [stdout]
 -r|--rasmol     fn      generate a rasmol script for the alignment
 -p|--path       fn      path to protein structures
 -h|--help               display this message
 
To visualize alignment under [[Linux]]:
 % rasmol -script rasmol-script

==References==
<references/>

==See also==
*[[wikipedia:Root mean square deviation (bioinformatics)]]
*[[RasMol]]

==External links==
*[http://biowulf.bu.edu/FAST/ Official website]

[[Category:Bioinformatics]]