Bio::Tools OddCodes
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Tools::OddCodes - Object holding alternative alphabet coding for
one protein sequence
Package variables
No package variables defined.
Inherit
Bio::Root::Root
Synopsis
  # 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$new_coding";
Description
Bio::Tools::Oddcodes is a welterweight object for rewriting a protein
sequence in an alternative alphabet. Eight of these are provided, ranging
from the the 2-letter hydrophobic alphabet, to the 8-letter chemical
alphabet. These are useful for the statistical analysis of protein
sequences since they can partially avoid the combinatorial explosion
produced by the full 20-letter alphabet (eg. 400 dimers, 8000 trimers
etc.)
The objects will print out a warning if the input sequence is not a
protein. If you know what you are doing, you can silence the warning
by setting verbose() to a negative value.
See SYNOPSIS above for object creation code.
Methods
new
No description
Code
structural()
No description
Code
functional()
No description
Code
hydrophobic()
No description
Code
Dayhoff()
No description
Code
Sneath()
No description
Code
Stanfel()
No description
Code
chemical()
No description
Code
charge()
No description
Code
_pullseq
No description
Code
Methods description
None available.
Methods code
newdescriptionprevnextTop
sub new {
    my($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;
}
structural()descriptionprevnextTop
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
}
functional()descriptionprevnextTop
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
}
hydrophobic()descriptionprevnextTop
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
}
Dayhoff()descriptionprevnextTop
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
}
Sneath()descriptionprevnextTop
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
}
Stanfel()descriptionprevnextTop
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
}
chemical()descriptionprevnextTop
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
}
charge()descriptionprevnextTop
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
}
_pullseqdescriptionprevnextTop
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;
}
General documentation
REFERENCESTop
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.
FEEDBACKTop
Mailing ListsTop
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
Reporting BugsTop
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:
  http://bugzilla.open-bio.org/
AUTHORTop
Derek Gatherer
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
structuralTop
 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
functionalTop
 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
hydrophobicTop
 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
DayhoffTop
 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
SneathTop
 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
StanfelTop
 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
chemicalTop
 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
chargeTop
 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