[EMBOSS] pepstats pI values (vs protparam)

[Peter Rice]

On 24/06/10 11:20, Ingo P. Korndoerfer wrote:
> oh no ... i need some help again ...
> 
> my colleagues tell me (similar to the issue resolved last week)
> peptstats and protparam calculate different pIs.
> 
> i could not find in the pepstats docu, how it calculates the pI. the
> file eamino.dat does not seem to contain any pKas,
> and i could not identify any other file by name that would contain pkas.

Ah, fixed file not currently available as a command line option.

Epk.dat is the file


> i any case, my feeling is i would have to manipulate some input to feed
> pepstats the values from
> 
> *Reference points for comparisons of two-dimensional maps of proteins
> from different human cell types defined in a pH scale where isoelectric
> points correlate with polypeptide compositions*
> Electrophoresis
> Volume 15, Issue 1, Date: 1994, Pages: 529-539
> Bengt Bjellqvist, Bodil Basse, Eydfinnur Olsen, Julio E. Celis
> 
> since this seems to be what protparam uses.

Ah, they have a few extra tricks, adjusting the N terminal values for
some amino acid residues.

So some coding changes (not much, but we are very close to the release
on July 15th) will be needed to implement these values.

Thanks for letting us know.

regards,

Peter Rice