Héctor Valverde > Mecom-1.11 > Mecom

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Module Version: 1.11   Source  

NAME ^

Mecom - A Perl module for protein contact interfaces evolutive analysis

VERSION ^

Version 1.11

SYNOPSIS ^

    # Create the object
    my $coe = Mecom->new(
                                    pdb         => 'pdb/files/path/2occ.pdb',
                                    alignment   => 'aln/files/path/chainM.aln',
                                    chain       => 'M',
                                    );
    # Run calcs
    $coe->run;
    
    # Write HTML Report
    open REP, ">report.html";
    print REP $coe->run_report;
    close REP;

DESCRIPTION ^

This module integrates a workflow aimed to address the evolvability of the contact interfaces within a protein complex. The method Mecom->run launchs the whole analysis. Also, such workflow is divided into the following steps:

Step 1, Structural analysis: Mecom->run_struct
Step 2, Sub-sets filtering: Mecom->run_filtering
Step 3, Sub-alignments building: Mecom->run_subalign
Step 4, Evolutionary calcs: Mecom->run_yang
Step 5, Statistical analysis: Mecom->run_stats1

A detailed explanation about these methods is reported below.

REQUERIMENTS ^

Bioperl
Bioperl-run
PAML
DSSP

CONSTRUCTOR ^

new()

    $obj = Mecom->new(%input_data);

The new class method construct a new Mecom object. The returned object can be used to perform several evolutive analysis. new accepts the following parameters in an input hash as above used %input_data:

MAIN METHODS ^

run()

    Title   : run
    Usage   : $obj->run
    Function: Launch the whole workflow analysis
    Returns : 
    Args    :

run_struct()

    Title   : run_struct
    Usage   : $obj->run_struct
    Function: Launch structural analysis and stores the result in the attribute:
              "structdata"
    Returns : True if success
    Args    :

run_filtering()

    Title   : run_struct
    Usage   : $obj->run_filtering
    Function: Build different categories of sets (Contact, NonContact ...)
              and set the attribute "lists" with the result
    Returns : True if success
    Args    :

run_subalign()

    Title   : run_subalign
    Usage   : $obj->run_subalign
    Function: Build new alignments from the input chain alignment and the categories
              built by run_filtering method. Stores the result into "subalns" attribute
    Returns : True if success
    Args    :

run_yang()

    Title   : run_yang
    Usage   : $obj->run_yang
    Function: Launch PAML for each alignment stored at "sub_alns" attribute and
              store the results into "paml_res"
    Returns : True if success
    Args    :

run_stats1()

    Title   : run_stats1
    Usage   : $obj->run_stats1
    Function: Run a Z-Test with the obtained evolutionary data and store the
              results into "stats" attribute
    Returns : True if success
    Args    :

run_report()

    Title   : run_report
    Usage   : $obj->run_report
    Function: Write a HTML report
    Returns : [String] HTML report with the results and input data
    Args    :

AUXILIAR METHODS ^

cat_aln()

    Title   : run_report
    Usage   : $obj->cat_aln(@alns)
    Function: Concatenates alignment objects. Sequences are identified by id.
             An error will be thrown if the sequence ids are not unique in the
             first alignment. If any ids are not present or not unique in any
             of the additional alignments then those sequences are omitted from
             the concatenated alignment, and a warning is issued. An error will
             be thrown if any of the alignments are not flush, since
             concatenating such alignments is unlikely to make biological
             sense.
    Returns : A unique Bio::SimpleAlign object
    Args    : A list of Bio::SimpleAlign objects

PROCESSED DATA STORAGE ^

Once each analysis has been performed, the resulting data is stored in other setable attributes:

SECONDARY METHODS (but not less important) ^

All attributes are accesible and mutable from methods called get_attribute and set_attribute, respectively. For example:

    # Set the proximity threshold ("pth") to 3 Angstroms
    $obj->set_pth(3);
    # Print the current value of the attribute "pth"
    print $obj->get_pth;

The processed data is also stored in attributes. Thus, this kind of methods can also be used to access and modify the results.

AUTHOR - Hector Valverde ^

Hector Valverde, <hvalverde@uma.es>

CONTRIBUTORS ^

Juan Carlos Aledo, <caledo@uma.es>

BUGS ^

Please report any bugs or feature requests to bug-Mecom-Complex at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Mecom-Complex. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

SUPPORT ^

This module is the program core of MECOM Perl program. Further information about this project is available at:

    http://mecom.hval.es/

You can find documentation for this module with the UNIX man command.

    man Mecom

LICENSE AND COPYRIGHT ^

Copyright 2013 Hector Valverde and Juan Carlos Aledo.

This program is free software; you can redistribute it and/or modify it under the terms of either: the GNU General Public License as published by the Free Software Foundation; or the Artistic License.

See http://dev.perl.org/licenses/ for more information.

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