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
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