NAME

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

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)

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq