| 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:
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.
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:
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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
| 2018-10-27 | perl v5.26.2 |