GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  BIO::TOOLS::ANALYSIS::PROTEIN::MITOPROT (3)

.ds Aq ’

NAME

Bio::Tools::Analysis::Protein::Mitoprot - a wrapper around Mitoprot server

CONTENTS

SYNOPSIS



  use Bio::Tools::Analysis::Protein::Mitoprot;

  use Bio::PrimarySeq;
  my $seq = Bio::PrimarySeq->new
    (-seq=>IKLCVHHJHJHJHJHJHJHNLAILAKAHLIELALAL,
     -primary_id=>test); # a Bio::PrimarySeqI object

  my $mitoprot = Bio::Tools::Analysis::Protein::Mitoprot->new
     ( -seq => $seq
     ); # sequence must be  >!5aa long and start with an M.

  # run Mitoprot prediction on a DNA sequence
  my $mitoprot->run();


  die "Could not get a result" unless $mitoprot->status =~ /^COMPLETED/;

  print $mitoprot->result;     # print raw prediction to STDOUT

  foreach my $feat ( $mitoprot->result(Bio::SeqFeatureI) ) {

      # do something to SeqFeature
      # e.g. print as GFF
      print $feat->gff_string, "\n";
      # or store within the sequence - if it is a Bio::RichSeqI
      $seq->add_SeqFeature($feat);

 }



DESCRIPTION

This class is a wrapper around the Mitoprot web server which calculates the probability of a sequence containing a mitochondrial targetting peptide. See http://mips.gsf.de/cgi-bin/proj/medgen/mitofilter for more details.

The results can be obtained in 3 formats:
1. The raw text of the program output



  my $rawdata = $analysis_object->result;



2. An reference to a hash of scores :



  my $data_ref = $analysis_object->result(parsed); print "predicted
  export prob is $data_ref->{export_prob}\n"; #



key values of returned hash are input_length, basic_aas, acidic_aas, export_prob, charge, cleavage_site.

3. A Bio::SeqFeature::Generic object



  my $ft = $analysis_object->result(Bio::SeqFeatureI);
  print "export prob is ", ($ft->each_tag_value(export_prob))[0]  ,"\n";



This the second implentation of Bio::SimpleAnalysisI which hopefully will make it easier to write wrappers on various services. This class uses a web resource and therefore inherits from Bio::WebAgent.

SEE ALSO

Bio::SimpleAnalysisI, Bio::Tools::Analysis::SimpleAnalysisBase, Bio::WebAgent

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 one of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the web:



  https://github.com/bioperl/bioperl-live/issues



AUTHORS

Richard Adams, Richard.Adams@ed.ac.uk,

APPENDIX

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

    result



 Usage   : $job->result (...)
 Returns : a result created by running an analysis
 Args    : various



The method returns a result of an executed job. If the job was terminated by an error the result may contain an error message instead of the real data.

This implementation returns differently processed data depending on argument:
undef Returns the raw ASCII data stream but without HTML tags
Bio::SeqFeatureI The argument string defines the type of bioperl objects returned in an array. The objects are Bio::SeqFeature::Generic. Feature primary tag is SigSeq. Feature tags are input_length , basic_aas, acidic_aas, export_prob, charge, cleavage_site, method.
’parsed’ hash references of parsed results { input_length =>, basic_aas=>, acidic_aas=>, export_prob=>, charge=>, cleavage_site=>}.

Search for    or go to Top of page |  Section 3 |  Main Index


perl v5.20.3 BIO::TOOLS::ANALYSIS::PROTEIN::MITOPROT (3) 2016-04-05

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.