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Man Pages


Manual Reference Pages  -  BIO::TOOLS::HMMER::SET (3)

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NAME

Bio::Tools::HMMER::Set - Set of identical domains from HMMER matches

CONTENTS

SYNOPSIS



    # get a Set object probably from the results object
    print "Bits score over set ",$set->bits," evalue ",$set->evalue,"\n";

    foreach $domain ( $set->each_Domain ) {
        print "Domain start ",$domain->start," end ",$domain->end,"\n";
    }



DESCRIPTION

Represents a set of HMMER domains hitting one sequence. HMMER reports two different scores, a per sequence total score (and evalue) and a per domain score and evalue. This object represents a collection of the same domain with the sequence bits score and evalue. (these attributes are also on the per domain scores, which you can get there).

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



AUTHOR - Ewan Birney

Email birney-at-ebi.ac.uk

APPENDIX

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

    add_Domain



 Title   : add_Domain
 Usage   : $set->add_Domain($domain)
 Function: adds the domain to the list
 Returns : nothing
 Args    : A Bio::Tools::HMMER::Domain object



    each_Domain



 Title   : each_Domain
 Usage   : foreach $domain ( $set->each_Domain() )
 Function: returns an array of domain objects in this set
 Returns : array
 Args    : none



    name



 Title   : name
 Usage   : $obj->name($newval)
 Function:
 Example :
 Returns : value of name
 Args    : newvalue (optional)



    desc



 Title   : desc
 Usage   : $obj->desc($newval)
 Function:
 Example :
 Returns : value of desc
 Args    : newvalue (optional)



    accession



 Title   : accession
 Usage   : $obj->accession($newval)
 Function:
 Example :
 Returns : value of accession
 Args    : newvalue (optional)



    bits



 Title   : bits
 Usage   : $obj->bits($newval)
 Function:
 Example :
 Returns : value of bits
 Args    : newvalue (optional)



    evalue



 Title   : evalue
 Usage   : $obj->evalue($newval)
 Function:
 Example :
 Returns : value of evalue
 Args    : newvalue (optional)



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perl v5.20.3 BIO::TOOLS::HMMER::SET (3) 2016-04-05

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