[EMBOSS] pepstats vs protparam

[Peter Rice]

On 18/06/2010 08:58, Ingo P. Korndoerfer wrote:
> we now noted that pepstats does give different values for absorption
> coefficients for the same sequence.
> i have looked at the pepstats docu but could not find anything on the
> algorithm used. really, the math seems simple
>
>   E(Prot) = Numb(Tyr)*Ext(Tyr) + Numb(Trp)*Ext(Trp) + Numb(Cystine)*Ext(Cystine)
>
> with
>
>   Ext(Tyr) = 1490, Ext(Trp) = 5500, Ext(Cystine) = 125;
>
> (from the protparam docu).
>
> would anybody know whether this is what pepstats uses (and help me avoid having to dig through the source code).

EMBOSS takes values from local data file emboss/data/Eamino.dat which is 
using slightly different values.

That file credits Gill and von Hippel(1989) _Anal_Biochem_ 182 319-326 for 
the extinction coefficient values.

Protparam updates these values from Pace et al. (1995). We will update 
EMBOSS to use these values in the next release.

Thanks for letting us know

Peter