http://wiki.christophchamp.com/index.php?action=history&feed=atom&title=FAST_Alignment_and_Search_Tool 2026-04-30T14:01:46Z Revision history for this page on the wiki MediaWiki 1.26.2 http://wiki.christophchamp.com/index.php?title=FAST_Alignment_and_Search_Tool&diff=3296&oldid=prev 2007-02-10T01:54:35Z

<p></p> <p><b>New page</b></p><div>'''FAST Alignment and Search Tool''' (or, just '''FAST''') is a new algorithm for aligning three-dimensional structures of proteins.&lt;ref name=Zhu2005&gt;Zhu J, Weng Z (2005). FAST: a novel protein structure alignment algorithm. ''Proteins: Structure, Function and Bioinformatics (14):417-423''.&lt;/ref&gt; 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.<br /> <br /> FAST is developed by Jianhua Zhu at the Bioinformatics Program of Boston University.<br /> <br /> ==Usage==<br /> % fast protein1 protein2 [-r rasmol-script]<br /> <br /> %1 fn protein #1<br /> %2 fn protein #2<br /> -o|--out fn output file name [stdout]<br /> -r|--rasmol fn generate a rasmol script for the alignment<br /> -p|--path fn path to protein structures<br /> -h|--help display this message<br /> <br /> To visualize alignment under [[Linux]]:<br /> % rasmol -script rasmol-script<br /> <br /> ==References==<br /> &lt;references/&gt;<br /> <br /> ==See also==<br /> *[[wikipedia:Root mean square deviation (bioinformatics)]]<br /> *[[RasMol]]<br /> <br /> ==External links==<br /> *[http://biowulf.bu.edu/FAST/ Official website]<br /> <br /> [[Category:Bioinformatics]]</div>

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