| Bio::Tools::OddCodes(3pm) | User Contributed Perl Documentation | Bio::Tools::OddCodes(3pm) |
Bio::Tools::OddCodes - Object holding alternative alphabet coding for one protein sequence
# 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";
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.
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.
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Please direct usage questions or support issues to the mailing list:
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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.
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Derek Gatherer
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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
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
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
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
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
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
| 2020-10-28 | perl v5.30.3 |