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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 "\nMonomer counts using statistics object\n";
   $seq_stats  =  Bio::Tools::SeqStats->new(-seq=>$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},"\n";
   }
 
   # obtain the count directly without creating a new statistics object
   print "\nMonomer counts without statistics object\n";
   $hash_ref = Bio::Tools::SeqStats->count_monomers($seqobj);
   foreach $base (sort keys %$hash_ref) {
       print "Number of bases of type ", $base, "= ", 
          %$hash_ref->{$base},"\n";
   }
 
 
   # obtain hash of counts of each type of codon in a nucleic acid sequence
   print "\nCodon counts using statistics object\n";
   $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},"\n";
   }
 
   #  or
   print "\nCodon counts without statistics object\n";
   $hash_ref = Bio::Tools::SeqStats->count_codons($seqobj);
   foreach $base (sort keys %$hash_ref) {
       print "Number of codons of type ", $base, "= ", 
          %$hash_ref->{$base},"\n";
   }
 
   # 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 "\nMolecular weight (using statistics object) of sequence ", 
           $seqobj->id(), " is between ", $$weight[0], " and " ,
           $$weight[1], "\n";
 
   #  or
   $weight = Bio::Tools::SeqStats->get_mol_wt($seqobj);
   print "\nMolecular weight (without statistics object) of sequence ", 
         $seqobj->id(), " is between ", $$weight[0], " and " ,
         $$weight[1], "\n";
 
   # 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:

*

The molecular weight of the sequence: get_mol_wt()

*

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

*

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

*

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:

   http://bugzilla.open-bio.org/
 
 

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.