[Bioperl-l] Bio::Seq weight ?

Heikki Lehvaslaiho heikki at ebi.ac.uk
Wed May 12 09:50:25 EDT 2004

On Tuesday 11 May 2004 19:14, stephan rosecker wrote:
> Hi,
> is it possible to get the weight form a Bio::Seq object ?

This is from the bptutorial script:

III.3.2 Obtaining basic sequence statistics (SeqStats,SeqWord)

In addition to the methods directly available in the Seq object,
bioperl provides various helper objects to determine additional
information about a sequence.  For example, SeqStats object provides
methods for obtaining the molecular weight of the sequence as well the
number of occurrences of each of the component residues (bases for a
nucleic acid or amino acids for a protein.)  For nucleic acids,
SeqStats also returns counts of the number of codons used.  For

  use SeqStats;
  $seq_stats  = Bio::Tools::SeqStats->new($seqobj);
  $weight = $seq_stats->get_mol_wt();
  $monomer_ref = $seq_stats->count_monomers();
  $codon_ref = $seq_stats->count_codons();  # for nucleic acid sequence

Note: sometimes sequences will contain ambiguous codes.  For this
reason, get_mol_wt() returns a reference to a two element array
containing a greatest lower bound and a least upper bound of the
molecular weight.


> regards,
> stephan
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> Bioperl-l at portal.open-bio.org
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