Bio::Tools::SeqStats(3pm)				User Contributed Perl Documentation				 Bio::Tools::SeqStats(3pm)

NAME

       Bio::Tools::SeqStats - Object holding statistics for one particular sequence

SYNOPSIS

	 # build a primary nucleic acid or protein sequence object somehow
	 # then build a statistics object from the sequence object

	 $seqobj = Bio::PrimarySeq->new(-seq	  => 'ACTGTGGCGTCAACTG',
					-alphabet => 'dna',
					-id	  => 'test');
	 $seq_stats  =	Bio::Tools::SeqStats->new(-seq => $seqobj);

	 # obtain a hash of counts of each type of monomer
	 # (i.e. amino or nucleic acid)
	 print "
Monomer counts using statistics object
";
	 $seq_stats  =	Bio::Tools::SeqStats->new(-seq=>$seqobj);
	 $hash_ref = $seq_stats->count_monomers();  # e.g. for DNA sequence
	 foreach $base (sort keys %$hash_ref) {
	     print "Number of bases of type ", $base, "= ",
		%$hash_ref->{$base},"
";
	 }

	 # obtain the count directly without creating a new statistics object
	 print "
Monomer counts without statistics object
";
	 $hash_ref = Bio::Tools::SeqStats->count_monomers($seqobj);
	 foreach $base (sort keys %$hash_ref) {
	     print "Number of bases of type ", $base, "= ",
		%$hash_ref->{$base},"
";
	 }

	 # obtain hash of counts of each type of codon in a nucleic acid sequence
	 print "
Codon counts using statistics object
";
	 $hash_ref = $seq_stats-> count_codons();  # for nucleic acid sequence
	 foreach $base (sort keys %$hash_ref) {
	     print "Number of codons of type ", $base, "= ",
		%$hash_ref->{$base},"
";
	 }

	 #  or
	 print "
Codon counts without statistics object
";
	 $hash_ref = Bio::Tools::SeqStats->count_codons($seqobj);
	 foreach $base (sort keys %$hash_ref) {
	     print "Number of codons of type ", $base, "= ",
		%$hash_ref->{$base},"
";
	 }

	 # Obtain the molecular weight of a sequence. Since the sequence
	 # may contain ambiguous monomers, the molecular weight is returned
	 # as a (reference to) a two element array containing greatest lower
	 # bound (GLB) and least upper bound (LUB) of the molecular weight
	 $weight = $seq_stats->get_mol_wt();
	 print "
Molecular weight (using statistics object) of sequence ",
		 $seqobj->id(), " is between ", $$weight[0], " and " ,
		 $$weight[1], "
";

	 #  or
	 $weight = Bio::Tools::SeqStats->get_mol_wt($seqobj);
	 print "
Molecular weight (without statistics object) of sequence ",
	       $seqobj->id(), " is between ", $$weight[0], " and " ,
	       $$weight[1], "
";

	 # Calculate mean Kyte-Doolittle hydropathicity (aka "gravy" score)
	 my $prot = Bio::PrimarySeq->new(-seq=>'MSFVLVAPDMLATAAADVVQIGSAVSAGS',
					 -alphabet=>'protein');
	 my $gravy = Bio::Tools::SeqStats->hydropathicity($seqobj);
	 print "might be hydropathic" if $gravy > 1;

DESCRIPTION

       Bio::Tools::SeqStats is a lightweight object for the calculation of simple statistical and numerical properties of a sequence. By
       "lightweight" I mean that only "primary" sequences are handled by the object.  The calling script needs to create the appropriate primary
       sequence to be passed to SeqStats if statistics on a sequence feature are required.  Similarly if a codon count is desired for a frame-
       shifted sequence and/or a negative strand sequence, the calling script needs to create that sequence and pass it to the SeqStats object.

       Nota that nucleotide sequences in bioperl do not strictly separate RNA and DNA sequences. By convention, sequences from RNA molecules are
       shown as is they were DNA. Objects are supposed to make the distinction when needed. This class is one of the few where this distinctions
       needs to be made. Internally, it changes all Ts into Us before weight and monomer count.

       SeqStats can be called in two distinct manners.	If only a single computation is required on a given sequence object, the method can be
       called easily using the SeqStats object directly:

	 $weight = Bio::Tools::SeqStats->get_mol_wt($seqobj);

       Alternately, if several computations will be required on a given sequence object, an "instance" statistics object can be constructed and
       used for the method calls:

	 $seq_stats = Bio::Tools::SeqStats->new($seqobj);
	 $monomers = $seq_stats->count_monomers();
	 $codons = $seq_stats->count_codons();
	 $weight = $seq_stats->get_mol_wt();
	 $gravy = $seq_stats->hydropathicity();

       As currently implemented the object can return the following values from a sequence:

       o   The molecular weight of the sequence: get_mol_wt()

       o   The number of each type of monomer present: count_monomers()

       o   The number of each codon present in a nucleic acid sequence: count_codons()

       o   The mean hydropathicity ("gravy" score) of a protein: hydropathicity()

       For DNA and RNA sequences single-stranded weights are returned. The molecular weights are calculated for neutral, or not ionized, nucleic
       acids. The returned weight is the sum of the base-sugar-phosphate residues of the chain plus one weight of water to to account for the
       additional OH on the phosphate of the 5' residue and the additional H on the sugar ring of the 3' residue.  Note that this leads to a
       difference of 18 in calculated molecular weights compared to some other available programs (e.g. Informax VectorNTI).

       Note that since sequences may contain ambiguous monomers (e.g. "M", meaning "A" or "C" in a nucleic acid sequence), the method get_mol_wt
       returns a two-element array containing the greatest lower bound and least upper bound of the molecule. For a sequence with no ambiguous
       monomers, the two elements of the returned array will be equal. The method count_codons() handles ambiguous bases by simply counting all
       ambiguous codons together and issuing a warning to that effect.

DEVELOPERS NOTES

       Ewan moved it from Bio::SeqStats to Bio::Tools::SeqStats

       Heikki made tiny adjustments (+/- 0.01 daltons) to amino acid molecular weights to have the output match values in SWISS-PROT.

       Torsten added hydropathicity calculation.

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 the web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Peter Schattner
       Email schattner AT alum.mit.edu

CONTRIBUTOR - Torsten Seemann
       Email torsten.seemann AT infotech.monash.edu.au

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   count_monomers
	Title	: count_monomers
	Usage	: $rcount = $seq_stats->count_monomers();
		  or $rcount = $seq_stats->Bio::Tools::SeqStats->($seqobj);
	Function: Counts the number of each type of monomer (amino acid or
		       base) in the sequence.
		  Ts are counted as Us in RNA sequences.
	Example :
	Returns : Reference to a hash in which keys are letters of the
		  genetic alphabet used and values are number of occurrences
		  of the letter in the sequence.
	Args	: None or reference to sequence object
	Throws	: Throws an exception if type of sequence is unknown (ie amino
		  or nucleic)or if unknown letter in alphabet. Ambiguous
		  elements are allowed.

   get_mol_wt
	Title	: get_mol_wt
	Usage	: $wt = $seqobj->get_mol_wt() or
		  $wt = Bio::Tools::SeqStats ->get_mol_wt($seqobj);
	Function: Calculate molecular weight of sequence
		  Ts are counted as Us in RNA sequences.
	Example :

	Returns : Reference to two element array containing lower and upper
		  bounds of molecule molecular weight. For DNA and RNA
		  sequences single-stranded weights are returned. If
		  sequence contains no ambiguous elements, both entries in
		  array are equal to molecular weight of molecule.
	Args	: None or reference to sequence object
	Throws	: Exception if type of sequence is unknown (ie not amino or
		  nucleic) or if unknown letter in alphabet. Ambiguous
		  elements are allowed.

   count_codons
	Title	: count_codons
	Usage	: $rcount = $seqstats->count_codons() or
		  $rcount = Bio::Tools::SeqStats->count_codons($seqobj)
	Function: Counts the number of each type of codons for a dna or rna
		  sequence, starting at the 1st triple of the input sequence.
	Example :
	Returns : Reference to a hash in which keys are codons of the genetic
		  alphabet used and values are number of occurrences of the
		  codons in the sequence. All codons with "ambiguous" bases
		  are counted together.
	Args	: None or sequence object
	Throws	: an exception if type of sequence is unknown or protein.

   hydropathicity
	Title	: hydropathicity
	Usage	: $gravy = $seqstats->hydropathicity(); or
		  $gravy = Bio::Tools::SeqStats->hydropathicity($seqobj);

	Function: Calculates the mean Kyte-Doolittle hydropathicity for a
		  protein sequence. Also known as the "gravy" score. Refer to
		  Kyte J., Doolittle R.F., J. Mol. Biol. 157:105-132(1982).
	Example :
	Returns : float
	Args	: None or reference to sequence object

	Throws	: an exception if type of sequence is not protein.

   _is_alphabet_strict
	Title	:  _is_alphabet_strict
	Usage	:
	Function: internal function to determine whether there are
		  any ambiguous elements in the current sequence
	Example :
	Returns : 1 if strict alphabet is being used,
		  0 if ambiguous elements are present
	Args	:

	Throws	: an exception if type of sequence is unknown (ie amino or
		  nucleic) or if unknown letter in alphabet. Ambiguous
		  monomers are allowed.

   _print_data
	Title	: _print_data
	Usage	: $seqobj->_print_data() or Bio::Tools::SeqStats->_print_data();
	Function: Displays dna / rna parameters (used for debugging)
	Returns : 1
	Args	: None

       Used for debugging.

perl v5.14.2							    2012-03-02						 Bio::Tools::SeqStats(3pm)