[Bioperl-l] swiss.pm again :)

Peter J Ulintz pulintz@umich.edu
Tue, 1 Aug 2000 08:49:38 -0400 (EDT)

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?


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)?