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]', -moltype = '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. 8 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.) See Synopsis above for object creation code.

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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 email or the web: bioperl-bugs@bioperl.org http://www.bioperl.org/bioperl-bugs/ Derek Gatherer 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 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 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 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 Returns : Reference to the new sequence string Args : none one protein sequence"