Bio::Tools::OddCodes(3pm) User Contributed Perl Documentation Bio::Tools::OddCodes(3pm)
NAME
Bio::Tools::OddCodes - Object holding alternative alphabet coding for one protein sequence
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 "
$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.
REFERENCES
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
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
Derek Gatherer
APPENDIX
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
perl v5.14.2 2012-03-02 Bio::Tools::OddCodes(3pm)