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)