[EMBOSS] pepstats vs protparam

[Ingo P. Korndoerfer]

dear fellow emboss users,

we have in the past used the wellknown expasy protparam tool to
calculate our extinction coefficients for proteins.
easy for most users and that is what they got used to. we are now
switching to an increased use of emboss, since
it can be so nicely incorporated into our database programs and pipelines.

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).
and second, it seems that the expasy colleagues have tweaked their algorithm further see

http://expasy.org/tools/protparam-doc.html 

(see the important note around the middle of the page).

would anybody have an opinion whether it would be adequate (even allowed) to emulate protparam behaviour in peptstats
or to give the user a choice to do so ? it seems this might be easy to code. for sure it would result in more consistency 
in our work and would also allow us to be more consistent in communication with our clients without having to move away 
from emboss.

thanks

cheers

ingo

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