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SmotifTF-0.09
River stage zero No dependents
++
/ Psipred

NAME

Psipred

VERSION

Version 0.01

SYNOPSIS

        Set of routines to run and analyze Psipred

        Usage: 

    use Psipred;

    run ($sequence, $directory);
    analyze_psipred ($pdb, $chain, $directory, $havestructure);

run

   run psipred
   /usr/local/bin/runpsipred 4wyq.fasta

analyze_psipred

It will return the secondary structure prediction and sequence from psipred output file.

Script to get the Smotif defintions from PSIPRED output

INPUT ARGUMENTS: 1) $pdb : pdb code (the PSIPRED output file should be in the subdirectory identified by the pdb code e.g. 1ptf/1ptf.horiz) 2) $chain : chain ID 3) If structure exists, 1, else, 0.

INPUT FILES: In the <pdbcode> folder: 1)<pdbcode>/<pdbcode>.horiz (PSIPRED output file) 2)<pdbcode>/pdb<pdbcode><chain>.ent (PDB file), if structure exists.

OUTPUT FILES: In the <pdbcode> folder: <pdbcode>.out :File with smotif information: Protein code, Chain, Smotif type, Smotif start residue, Loop length, Length of first secondary structure, Length of second secondary structure, Sequence

write_outfile

    Writes the smotif definitions obtained from Psipred to the $pdb/$pdb.out file

    Input: $filename, $seq, @ss
    This is the most important file and has to named $pdb/$pdb.out
    and the format of this file is 
    print OUTFILE "Name\tChain\tType\tStart\tLooplength\tSS1length\tSS2length\tSequence\n";

split_ss_string

SUBROUTINE to convert a series of secondary structure types to a list of start and end points for smotifs #Input 1: $ss - a string of secondary structure types, where H=alpha helix and E=strand e.g. (HHHHLLLLEEEE) #Input 2: $startpos - residue at which first smotif begins

getFirstResidueNumber

Subroutine to get starting residue number of a pdb file

parse

It returns a hash containing the following keys: $VAR1 = { 'AA' => 'MNLQPIFWIGLISSVCCVF...' 'Conf' => '9975402235541123446...' 'Pred' => 'CCCCCCHHHHHHHCEEEEE...' };

count_smotifs

Subroutine to count the number of Smotifs in a given Smotif definition file (typically $pdb/$pdb.out). Input : Filename with Smotif definition Output: Returns the number of Smotifs in the given file

count_pdb_smotifs

Subroutine to count the number of Smotifs in a given Smotif definition file (typically $pdb/$pdb.out). Input : Filename with Smotif definition Output: Returns the number of Smotifs in the given file

AUTHORS

Fiserlab Members , <andras at fiserlab.org>

BUGS

Please report any bugs or feature requests to bug-./ at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=./.

SUPPORT

You can find documentation for this module with the perldoc command.

    perldoc Psipred

LICENSE AND COPYRIGHT

Copyright 2015 Fiserlab Members .

This program is free software; you can redistribute it and/or modify it under the terms of the the Artistic License (2.0). You may obtain a copy of the full license at:

http://www.perlfoundation.org/artistic_license_2_0

Any use, modification, and distribution of the Standard or Modified Versions is governed by this Artistic License. By using, modifying or distributing the Package, you accept this license. Do not use, modify, or distribute the Package, if you do not accept this license.

If your Modified Version has been derived from a Modified Version made by someone other than you, you are nevertheless required to ensure that your Modified Version complies with the requirements of this license.

This license does not grant you the right to use any trademark, service mark, tradename, or logo of the Copyright Holder.

This license includes the non-exclusive, worldwide, free-of-charge patent license to make, have made, use, offer to sell, sell, import and otherwise transfer the Package with respect to any patent claims licensable by the Copyright Holder that are necessarily infringed by the Package. If you institute patent litigation (including a cross-claim or counterclaim) against any party alleging that the Package constitutes direct or contributory patent infringement, then this Artistic License to you shall terminate on the date that such litigation is filed.

Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.