NAME

Bio::Tools::Run::MCS - Wrapper for MCS

SYNOPSIS

  use Bio::Tools::Run::MCS;

  # Make a MCS factory
  $factory = Bio::Tools::Run::MCS->new();

  # Run MCS on an alignment
  my @results = $factory->run($alignfilename);

  # or with alignment object
  @results = $factory->run($bio_simplalign);

  # look at the results
  foreach my $feat (@results) {
    my $seq_id = $feat->seq_id;
    my $start = $feat->start;
    my $end = $feat->end;
    my $score = $feat->score;
    my ($pvalue) = $feat->get_tag_values('pvalue');
    my ($kind) = $feat->get_tag_values('kind'); # 'all', 'exon' or 'nonexon'
  }

DESCRIPTION

This is a wrapper for running the MCS (binCons) scripts by Elliott H Margulies. You can get details here: http://zoo.nhgri.nih.gov/elliott/mcs_doc/. MCS is used for the prediciton of transcription factor binding sites and other regions of the genome conserved amongst different species.

Note that this wrapper assumes you already have alignments, so only uses MCS for the latter stages (the stages involving align2binomial.pl, generate_phyloMAX_score.pl and generate_mcs_beta.pl).

You can try supplying normal MCS command-line arguments to new(), eg.

  $factory->new(-percentile => 95)

or calling arg-named methods (excluding the initial hyphens, eg.

  $factory->percentile(95)

 to set the --percentile arg).

You will need to enable this MCS wrapper to find the MCS scripts. This can be done in (at least) three ways:

 1. Make sure the MCS scripts are in your path.
 2. Define an environmental variable MCSDIR which is a 
    directory which contains the MCS scripts:
    In bash:

    export MCSDIR=/home/username/mcs/

    In csh/tcsh:

    setenv MCSDIR /home/username/mcs

 3. Include a definition of an environmental variable MCSDIR in
    every script that will use this MCS wrapper module, e.g.:

    BEGIN { $ENV{MCSDIR} = '/home/username/mcs/' }
    use Bio::Tools::Run::MCS;

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Sendu Bala

Email bix@sendu.me.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

program_name

 Title   : program_name
 Usage   : $factory>program_name()
 Function: holds the program name
 Returns : string
 Args    : None

program_dir

 Title   : program_dir
 Usage   : $factory->program_dir(@params)
 Function: returns the program directory, obtained from ENV variable.
 Returns : string
 Args    : None

new

 Title   : new
 Usage   : $factory = Bio::Tools::Run::MCS->new()
 Function: creates a new MCS factory
 Returns : Bio::Tools::Run::MCS
 Args    : Many options understood by MCS can be supplied as key =>
           value pairs.

           These options can NOT be used with this wrapper:
           ucsc gtf neutral-only fourd-align align-only ar

run

 Title   : run
 Usage   : $result = $factory->run($align_file_or_object, Bio::Location::Atomic,
                                   [Bio::SeqFeatureI]);
 Function: Runs the MCS scripts on an alignment.
 Returns : list of Bio::SeqFeatureI feature objects (with coordinates corrected
           according to the supplied offset, if any)
 Args    : The first argument represents an alignment, the optional second
           argument represents the chromosome, stand and end and the optional
           third argument represents annotation of the exons in the alignment.

           The alignment can be provided as a multi-fasta format alignment
           filename, or a Bio::Align::AlignI compliant object (eg. a
           Bio::SimpleAlign).

           The position in the genome can be provided as a Bio::Location::Atomic
           with start, end and seq_id set.

           The annnotation can be provided as an array of Bio::SeqFeatureI
           objects.

_setparams

 Title   : _setparams
 Usage   : Internal function, not to be called directly
 Function: Creates a string of params to be used in the command string
 Returns : string of params
 Args    : none