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SmotifTF-0.09
River stage zero No dependents
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/ CompareSmotifs

NAME

CompareSmotifs

VERSION

Version 0.01

SYNOPSIS

Subroutines to compare a given query Smotif to all the Smotifs in the dynamic database, compute e-values using the HHsuite and provide a list of suitable Smotifs based on the e-values.

    use CompareSmotifs;

    test_motif($pdb,$havestructure,$motnum);

SUBROUTINES

    test_motif
    check_pdb 
    get_evalue   
    trim 
    ltrim
    rtrim
    match_in_array 
    get_hhm 
    read_dd_info

test_motif

Subroutine to compare Smotifs from a query protein against a dynamic database of Smotifs using hidden markov model profiles.

INPUT ARGUMENTS 1) $pdb : 4-letter pdb code (with a directory in the current folder with the same name). 2) $havestructure : 0=no solved structure for RMSD comparison, 1=solved structure exists for RMSD comparison 3) $motnum : which smotif of the protein to compare (0=1st smotif, 1=2nd smotif, and so on)

INPUT FILES In the <pdbcode> folder: 1) <pdbcode>.out : Standard file with information about each Smotif - Smotif definitions 2)dd_info_evalue.out : File with information about all Smotifs in the dynamic database.

OUTPUT FILES In the <pdbcode> folder: 1) dd_shiftcands<pdbcode><motnum>_<looplength><smotif type>.csv : File containing results of comparing the query smotif against the database. Includes the number of residues compared, the e-values from HMM-HMM comparisons, the RMSD (if structure is included), the loop length, the smotif NID, the secondary structure RMSD, secondary structure lengths, and loop structural signatures for the query and database motif and their overlap.

check_pdb

Subroutine to check pdb file for missing residues and insertions.

get_evalue

Subroutine to get evalue given two sequences

match_in_array

Subroutine to find if a scalar element appears in an array

trim

Trim function to remove whitespace from the start and end of the string

ltrim

Left trim function to remove leading whitespace

rtrim

Right trim function to remove trailing whitespace

get_hhm

Subroutine to carry out HHblits and generate HMM for a sequence without adding SS info from DSSP or PSIPRED

read_dd_info

Subroutine to read the information from the dynamic database

AUTHORS

Fiserlab memebers, <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 CompareSmotifs

LICENSE AND COPYRIGHT

Copyright 2015 Brinda Vallat, Vilas Menon .

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.