/ 
bioperl-1.2.3
/ Bio::Tools::OddCodes

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. 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.

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://www.bioperl.org/MailList.html - About the mailing lists

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/

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 
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