[Bioperl-l] swiss.pm again :)

[Ewan Birney]

On Tue, 1 Aug 2000, Peter J Ulintz wrote:

> 
> Hi,
>         
> It appears as if the calculation in SeqStats.pm previously overestimated
> the mass due to water in the calculation of MW.  There's a loss of a water
> in forming each peptide bond, so the number of waters that have to be
> subtracted from the final mass of a peptide is (length-1).  This has been
> corrected by "kdj" in my version with the following lines in the 
> get_mol_wt subroutine, and gives the correct result:
>  
>    # Added by kdj: removal of H2O during peptide bond formation!
>    $weight_lower_bound -= $water * ($seqobj->length - 1);
>    $weight_upper_bound -= $water * ($seqobj->length - 1);
> 
> Would using the older version of SeqStats be the source of the problem?

Could well be. Lorenz - are you working on the main trunk or the branch -
in which case, SeqStats needs to be updated on whichever side this is not
been updated on


 > 
> --Pete
> 
> _______________________________________
> Peter Ulintz     Research Programmer
> Andrews Lab      University of Michigan
> 734.936.1327     pulintz@umich.edu
> 
> 
> > 
> > > > *) Molecular Weight is different to original (?)
> > >
> > > Could this be the starting Met?
> > 
> > Could that make a difference from ca. 38000 to ca. 43000 ??
> > 
> >      What does the SwissProt databank documentation say about the molecular
> >      weight? Would it account for and include post-translational
> >      modifications, like acylation and glycosylation? Could that be the
> >      case for the respective entry (i.e., is it a secreted or membrane
> >      protein)?
> > 
> 
> 
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