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 programs 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)