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:

         https://github.com/bioperl/bioperl-live/issues

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