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. 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.) 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 negetive value. 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.bugzilla.bioperl.org/ 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