/ 
bioperl-run-1.4
/ Bio::Tools::Run::Hmmpfam

NAME

Bio::Tools::Run::Hmmpfam

SYNOPSIS

Build a Hmmpfam factory

my @params = ('DB'=>$dbfile,'E'=>0.0001);
my $factory = Bio::Tools::Run::Hmmpfam->new($params);

# Pass the factory a Bio::Seq object or a file name

# returns a Bio::SearchIO object
my $search = $factory->run($seq);


my @feat;
while (my $result = $searchio->next_result){
 while(my $hit = $result->next_hit){
  while (my $hsp = $hit->next_hsp){
    push @feat, $hsp;
  }
 }
}

#Available params:
# n        : nucleic acid models/sequence (default protein)
# E <x>    : sets E value cutoff (globE) to <x>; default 10
# T <x>    : sets T bit threshold (globT) to <x>; no threshold by default
# Z <n>    : sets Z (# models) for E-value calculation

DESCRIPTION

Wrapper module for Hmmpfam program that allows one to search a sequence against an HMM database. Binary is available at http://hmmer.wustl.edu/

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://bio.perl.org/MailList.html             - About the mailing lists

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 email or the web:

bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/

AUTHOR - Bala

Email: bala@tll.org.sg

CONTRIBUTORS

Shawn Hoon shawnh@fugu-sg.org

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, obtiained from ENV variable.
Returns:  string
Args    :

new

Title   : new
Usage   : $hmmpfam->new(@params)
Function: creates a new Hmmpfam factory
Returns:  Bio::Tools::Run::Hmmpfam
Args    :

predict_protein_features

Title   :   predict_protein_features
Usage   :   DEPRECATED. Use obj->run($seqFile)
Function:   Runs Hmmpfam and creates an array of featrues
Returns :   An array of Bio::SeqFeature::Generic objects
Args    :   A Bio::PrimarySeqI

run

Title   :   run
Usage   :   $obj->run($seqFile)
Function:   Runs Hmmpfam and creates an array of featrues
Returns :   An array of Bio::SeqFeature::Generic objects
Args    :   A Bio::PrimarySeqI

_run

Title   :   _run
Usage   :   $obj->_run()
Function:   Internal(not to be used directly)
Returns :   An array of Bio::SeqFeature::Generic objects
Args    :

_setparams

Title   :  _setparams
Usage   :  Internal function, not to be called directly
Function:  creates a string of params to be used in the command string
Example :
Returns :  string of params
Args    :

_writeSeqFile

Title   :   _writeSeqFile
Usage   :   obj->_writeSeqFile($seq)
Function:   Internal(not to be used directly)
Returns :
Args    :