Bio::Tools::OddCodes(3)

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 "\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.

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:

  http://bugzilla.open-bio.org/

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