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Bio::Tools::OddCodes(3User Contributed Perl DocumentatiBio::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:

	 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

perl v5.32.0			  2019-12-07	       Bio::Tools::OddCodes(3)

NAME | SYNOPSIS | DESCRIPTION | REFERENCES | FEEDBACK | AUTHOR | APPENDIX

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