Bio::Tools::OddCodes - Object holding alternative alphabet coding for

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Tools::OddCodes - Object holding alternative alphabet coding for one protein sequence

SYNOPSIS

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  # Take a sequence object from eg, an inputstream, and creates an
  # object for the purposes of rewriting that sequence in another
  # alphabet.  These are abbreviated amino acid sequence alphabets,
  # designed to simplify the statistical aspects of analysing protein
  # sequences, by reducing the combinatorial explosion of the
  # 20-letter alphabet.  These abbreviated alphabets range in size
  # from 2 to 8.

  # Creating the OddCodes object, eg:

	my $inputstream = Bio::SeqIO->new( '-file' => "seqfile",
                                           '-format' => 'Fasta');
	my $seqobj = $inputstream->next_seq();
	my $oddcode_obj = Bio::Tools::Oddcodes->new(-seq => $seqobj);

  # or:

	my $seqobj = Bio::PrimarySeq->new
              (-seq=>'[cut and paste a sequence here]',
               -alphabet => 'protein',
               -id => 'test');
	my $oddcode_obj  =  Bio::Tools::OddCodes->new(-seq => $seqobj);

  # do the alternative coding, returning the answer as a reference to
  # a string

	my $output = $oddcode_obj->structural();
	my $output = $oddcode_obj->chemical();
	my $output = $oddcode_obj->functional();
	my $output = $oddcode_obj->charge();
	my $output = $oddcode_obj->hydrophobic();
	my $output = $oddcode_obj->Dayhoff();
	my $output = $oddcode_obj->Sneath();
	my $output = $oddcode_obj->Stanfel();




  # display sequence in new form, eg:

	my $new_coding = $$output;
	print "\n$new_coding";

DESCRIPTION

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Bio::Tools::Oddcodes is a welterweight object for rewriting a protein sequence in an alternative alphabet. Eight of these are provided, ranging from the the 2-letter hydrophobic alphabet, to the 8-letter chemical alphabet. These are useful for the statistical analysis of protein sequences since they can partially avoid the combinatorial explosion produced by the full 20-letter alphabet (eg. 400 dimers, 8000 trimers etc.)

The objects will print out a warning if the input sequence is not a protein. If you know what you are doing, you can silence the warning by setting verbose() to a negative value.

See SYNOPSIS above for object creation code.

REFERENCES

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Stanfel LE (1996) A new approach to clustering the amino acids. J. theor. Biol. 183, 195-205.

Karlin S, Ost F and Blaisdell BE (1989) Patterns in DNA and amino acid sequences and their statistical significance. Chapter 6 of: Mathematical Methods for DNA Sequences. Waterman MS (ed.) CRC Press, Boca Raton , FL.

FEEDBACK

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

AUTHOR

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Derek Gatherer

APPENDIX

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

structural

 Title   : structural
 Usage   : $output = $oddcode_obj->structural();
 Function: turns amino acid sequence into 3-letter structural alphabet
	 : A (ambivalent), E (external), I (internal)
 Example : a sequence ACDEFGH will become AAEEIAE
 Returns : Reference to the new sequence string
 Args    : none

functional

 Title   : functional
 Usage   : $output = $oddcode_obj->functional();
 Function: turns amino acid sequence into 4-letter functional alphabet
	 : A (acidic), C (basic), H (hydrophobic), P (polar)
 Example : a sequence ACDEFGH will become HPAAHHC
 Returns : Reference to the new sequence string
 Args    : none

hydrophobic

 Title   : hydrophobic
 Usage   : $output = $oddcode_obj->hydrophobic();
 Function: turns amino acid sequence into 2-letter hydrophobicity alphabet
	 : O (hydrophobic), I (hydrophilic)
 Example : a sequence ACDEFGH will become OIIIOII
 Returns : Reference to the new sequence string
 Args    : none

Dayhoff

 Title   : Dayhoff
 Usage   : $output = $oddcode_obj->Dayhoff();
 Function: turns amino acid sequence into 6-letter Dayhoff alphabet
 Example : a sequence ACDEFGH will become CADDGCE
         : A (=C),   C (=AGPST), D (=DENQ),
         : E (=HKR), F (=ILMV),  G (=FWY)
 Returns : Reference to the new sequence string
 Args    : none

Sneath

 Title   : Sneath
 Usage   : $output = $oddcode_obj->Sneath();
 Function: turns amino acid sequence into 7-letter Sneath alphabet
 Example : a sequence ACDEFGH will become CEFFHCF
         : A (=ILV), C (=AGP), D (=MNQ), E (=CST),
         : F (=DE),  G (=KR),  H (=FHWY)
 Returns : Reference to the new sequence string
 Args    : none

Stanfel

 Title   : Stanfel
 Usage   : $output = $oddcode_obj->Stanfel();
 Function: turns amino acid sequence into 4-letter Stanfel alphabet
 Example : a sequence ACDEFGH will become AACCDAE
         : A (=ACGILMPSTV), C (=DENQ), D (=FWY), E (=HKR)
 Returns : Reference to the new sequence string
 Args    : none

chemical

 Title   : chemical
 Usage   : $output = $oddcode_obj->chemical();
 Function: turns amino acid sequence into 8-letter chemical alphabet
	 : A (acidic), L (aliphatic), M (amide), R (aromatic)
	 : C (basic),  H (hydroxyl),  I (imino), S (sulphur)
 Example : a sequence ACDEFGH will become LSAARAC
 Returns : Reference to the new sequence string
 Args    : none

charge

 Title   : charge
 Usage   : $output = $oddcode_obj->charge();
 Function: turns amino acid sequence into 3-letter charge alphabet
 Example : a sequence ACDEFGH will become NNAANNC
         : A (negative; NOT anode), C (positive; NOT cathode), N (neutral)
 Returns : Reference to the new sequence string
 Args    : none
BioPerl documentation Contained in the BioPerl distribution. 
#$Id$
#-----------------------------------------------------------------------------
# PACKAGE    : OddCodes.pm
# PURPOSE    : To write amino acid sequences in alternative alphabets
# AUTHOR     : Derek Gatherer (D.Gatherer@organon.nhe.akzonobel.nl)
# SOURCE     :
# CREATED    : 8th July 2000
# MODIFIED   :
# DISCLAIMER : I am employed in the pharmaceutical industry but my
#            : employers do not endorse or sponsor this module
#            : in any way whatsoever.  The above email address is
#            : given purely for the purpose of easy communication
#            : with the author, and does not imply any connection
#	     : between my employers and anything written below.
# LICENCE    : You may distribute this module under the same terms
#	     : as the rest of BioPerl.
#----------------------------------------------------------------------------


package Bio::Tools::OddCodes;
use strict;


use base qw(Bio::Root::Root);

sub new
{
    my($class,@args) = @_;

    my $self = $class->SUPER::new(@args);

    my ($seqobj) = $self->_rearrange([qw(SEQ)],@args);
    if((! defined($seqobj)) && @args && ref($args[0])) {
	# parameter not passed as named parameter?
	$seqobj = $args[0];
    }
    unless  ($seqobj->isa("Bio::PrimarySeqI"))
    {
        $self->throw("Bio::Tools::OddCodes only works on PrimarySeqI objects");
    }

    $self->{'_seqref'} = $seqobj;

    return $self;
}


sub structural()
{
	my $self = $_[0];
	my $seqstring = &_pullseq($self);	# see _pullseq() below

# now the real business

	$seqstring =~ tr/[ACGPSTWY]/1/;
	$seqstring =~ tr/[RNDQEHK]/2/;
	$seqstring =~ tr/[ILMFV]/3/;
	$seqstring =~ tr/1/A/;
	$seqstring =~ tr/2/E/;
	$seqstring =~ tr/3/I/;

	return \$seqstring;

# and that's that one
}


sub functional()
{
	my $self = $_[0];
	my $seqstring = &_pullseq($self);

# now the real business

	$seqstring =~ tr/[DE]/1/;
	$seqstring =~ tr/[HKR]/2/;
	$seqstring =~ tr/[AFILMPVW]/3/;
	$seqstring =~ tr/[CGNQSTY]/4/;
	$seqstring =~ tr/1/A/;
	$seqstring =~ tr/2/C/;
	$seqstring =~ tr/3/H/;
	$seqstring =~ tr/4/P/;

	return \$seqstring;

# and that's that one
}


sub hydrophobic()
{
	my $self = $_[0];
	my $seqstring = &_pullseq($self);

# now the real business

	$seqstring =~ tr/[AFILMPVW]/1/;
	$seqstring =~ tr/[CDEGHKNQRSTY]/2/;
	$seqstring =~ tr/1/I/;
	$seqstring =~ tr/2/O/;

	return \$seqstring;

# and that's that one
}


sub Dayhoff()
{
	my $self = $_[0];
	my $seqstring = &_pullseq($self);

# now the real business

	$seqstring =~ tr/[C]/1/;
	$seqstring =~ tr/[AGPST]/2/;
	$seqstring =~ tr/[DENQ]/3/;
	$seqstring =~ tr/[HKR]/4/;
	$seqstring =~ tr/[ILMV]/5/;
	$seqstring =~ tr/[FWY]/6/;
	$seqstring =~ tr/1/A/;
	$seqstring =~ tr/2/C/;
	$seqstring =~ tr/3/D/;
	$seqstring =~ tr/4/E/;
	$seqstring =~ tr/5/F/;
	$seqstring =~ tr/6/G/;

	return \$seqstring;

# and that's that one
}


sub Sneath()
{
	my $self = $_[0];
	my $seqstring = &_pullseq($self);

# now the real business

	$seqstring =~ tr/[ILV]/1/;
	$seqstring =~ tr/[AGP]/2/;
	$seqstring =~ tr/[MNQ]/3/;
	$seqstring =~ tr/[CST]/4/;
	$seqstring =~ tr/[DE]/5/;
	$seqstring =~ tr/[KR]/6/;
	$seqstring =~ tr/[FHWY]/7/;
	$seqstring =~ tr/1/A/;
	$seqstring =~ tr/2/C/;
	$seqstring =~ tr/3/D/;
	$seqstring =~ tr/4/E/;
	$seqstring =~ tr/5/F/;
	$seqstring =~ tr/6/G/;
	$seqstring =~ tr/7/H/;

	return \$seqstring;

# and that's that one
}


sub Stanfel()
{
	my $self = $_[0];
	my $seqstring = &_pullseq($self);

# now the real business

	$seqstring =~ tr/[ACGILMPSTV]/1/;
	$seqstring =~ tr/[DENQ]/2/;
	$seqstring =~ tr/[FWY]/3/;
	$seqstring =~ tr/[HKR]/4/;
	$seqstring =~ tr/1/A/;
	$seqstring =~ tr/2/C/;
	$seqstring =~ tr/3/D/;
	$seqstring =~ tr/4/E/;

	return \$seqstring;

# and that's that one
}


sub chemical()
{
	my $self = $_[0];
	my $seqstring = &_pullseq($self);

# now the real business

	$seqstring =~ tr/[DE]/1/;
	$seqstring =~ tr/[AGILV]/2/;
	$seqstring =~ tr/[NQ]/3/;
	$seqstring =~ tr/[FWY]/4/;
	$seqstring =~ tr/[RHK]/5/;
	$seqstring =~ tr/[ST]/6/;
	$seqstring =~ tr/P/7/;
	$seqstring =~ tr/[CM]/8/;
	$seqstring =~ tr/1/A/;
	$seqstring =~ tr/2/L/;
	$seqstring =~ tr/3/M/;
	$seqstring =~ tr/4/R/;
	$seqstring =~ tr/5/C/;
	$seqstring =~ tr/6/H/;
	$seqstring =~ tr/7/I/;
	$seqstring =~ tr/8/S/;

	return \$seqstring;

# and that's that one
}


sub charge()
{
	my $self = $_[0];
	my $seqstring = &_pullseq($self);

# now the real business

	$seqstring =~ tr/[DE]/1/;
	$seqstring =~ tr/[HKR]/2/;
	$seqstring =~ tr/[ACFGILMNPQSTVWY]/3/;
	$seqstring =~ tr/1/A/;
	$seqstring =~ tr/2/C/;
	$seqstring =~ tr/3/N/;

	return \$seqstring;

# and that's that one
}

# _pullseq is called within each of the subroutines
# it just checks a few things and returns the sequence

sub _pullseq
{
	my $self = $_[0];

	my $seqobj =  $self->{'_seqref'};

	unless  ($seqobj->isa("Bio::PrimarySeqI"))
	{
		$self->throw("die, OddCodes works only on PrimarySeqI objects\n");
    	}
        $self->warn("\tAll OddCode alphabets need a protein sequence,\n".
                    "\tbut BioPerl thinks this is not: [". $seqobj->id. "]")
            unless $seqobj->alphabet eq 'protein' or $self->verbose < 0;;

	my $seqstring = uc $seqobj->seq();

	if(length($seqstring)<1)
	{
		$self->throw("$seqstring: die, sequence has zero length\n");
	}
	return $seqstring;
}

1;