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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