THESEUS_ALIGN(1)					      General Commands Manual						  THESEUS_ALIGN(1)

NAME

       theseus_align - quick-and-dirty way to superimpose proteins

SYNOPSIS

       theseus_align [theseus options] -f pdbfile1.pdb pdbfile2.pdb ...

OPTIONS

       The options given to the script will be passed on to theseus. For a complete description, see the man page for theseus (1).

DESCRIPTION

       This  manual  page briefly documents briefly the script theseus_align, designed for a quick-and-dirty way to ML superposition proteins with
       different sequences. It should work very well when the protein sequences are relatively similar, although the ML  method  will  still  give
       much  better  results  than least-squares when the sequences are moderately divergent.  Technically, this procedure gives a structure-based
       superposition of a sequence-based alignment. It does not perform a structure-based alignment.

       First, the script uses theseus to create FASTA formatted sequence files corresponding to the exact protein sequences found in the pdb files
       that you supply.

       Second,	these  sequences  are  aligned using the multiple sequence alignment program of your choice. The script can easily be modified for
       CLUSTALW, T_COFFEE, KALIGN, DIALIGN2, or MAFFT. Any multiple sequence alignment program can be used, as long as it  can	generate  clustal-
       formatted  files.  However,  I  highly  recommend  Bob  Edgar's	MUSCLE	program  for  both  its  speed	and  accuracy.	(For more info see
       http://www.drive5.com/muscle/ .)

       Third, theseus performs a superposition of the structures using the sequence alignment as a guide.

       The installed version of theseus_align uses muscle (1) for doing the multiple sequence alignment. If you wish to use one of the other  pro-
       grams mentioned above, you'll have to copy the script to your own directory and edit it.

SEE ALSO

       theseus (1), muscle (1), clustalw (1), t_coffee (1), kalign (1), dialign2 (1), mafft (1).  All of these programs can be installed on Debian
       or Ubuntu systems using apt-get (8).

AUTHOR

       theseus_align was written by Douglas L. Theobald, Department of Biochemistry, Brandeis University.

								  November, 2008						  THESEUS_ALIGN(1)