[Bioperl-l] Bio::Seq weight ?

[Heikki Lehvaslaiho]

The current parsers do not read it in at all. The value is recreated using the 
Bio::Tools::SeqStats::get-mol_wt() for output.

Is this crucial? What do you need it for? There are so many value sets that 
differ from each other very slightly that the last digit in hardly 
meaningful. If you need to verify the identity, use the checksum.

I guess I could find out what are the amino acid weights used by SWISS-PROT 
programs and replace them in the SeqStats class. Is anyone relying heavily on 
current values?

	-Heikki

On Wednesday 12 May 2004 07:08, stephan rosecker wrote:
> thx,
> but i use it already.
> I want the weight from the original entry for example in swissprot the
>   	Molecular weight enrty.
>
> SQ   SEQUENCE   403 AA;  45542 MW;  BC433B2D29587383 CRC64;
>       MEELGLATAK VTVTKEASHH READLYQKMK SLESKLDFFN IQEEYIKYEY KNLKRELLHA
>       QEEVKRIRSV PLLIGQLLEM VDSNTGIVQS TSGSTLCVRI LSTIDRELLK PSASVALQRH
>       SNALVDTLPP ESDSSIHLLG ADEKPSESYS DIGGGDIQKQ EMREAVELPL THHNLYKQIG
>       IDPPRGVLLY GPPGTGKTML AKAVAHHTSA AFIRVVGSEF VQKYLGEGPR LVRDVFRLAR
>       ENSPAIIFID EIDAIATKRF DAQTGADREV QRILMELLNQ MDGFDVSVNV KVIMATNRQD
>       TLDPALLRPG RLDRKIEFPL PDRRQKRLIF QVITSKMNLS DEVDLEDYVS RPDKLSGAEI
>       QSICQEAGMH AIRKNRYVIL PKDFEKGYKA SIKKNTHEFN FYN
>
>
> =>(45542 MW) i want this.
> get_mol_wt() differs.
>
>
>
> regards,
> stephan
>
> Heikki Lehvaslaiho wrote:
> > 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
> > example:
> >
> >   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.
> >
> >
> > 	-Heikki
> >
> >>regards,
> >>stephan
> >>_______________________________________________
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> >>Bioperl-l at portal.open-bio.org
> >>http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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