Peter Rice ricepeterm at yahoo.co.uk
Sun Dec 23 09:04:14 UTC 2012

On 21/12/2012 16:26, Vasudevan, Geetha wrote:
>>> I have been trying to figure out the origin for the difference in computed pI
>>> value between EMBOSS-IEP (or EMBOSS-PEPSTATS) and Vector NTI (which uses
>> Expasy Compute pI/MW).
>>> I get 7.07 with EMBOSS and 6.65 with Expasy. I also tried the web site of
>> Expasy and I get the same as VectorNTI.
>>> Do you know the origin of the variation?

We use amino acid data values calculated for native amino acids. Expasy 
uses values calculated from protein isoelectric focussing (e.g. for 2D 
gels) under specific conditions, with a note that for highly basic 
proteins these values may not approximate experimentally determined values.

There are multiple possible data values that can be used for isoelectric 
point calculations, for example Wikipedia gives a third set without 

You can choose your own pKa values for each amino acid by using a local 
copy of file Epk.dat.

For the next release we will add further documentation on the origin of 
the default values used by EMBOSS, and may add a choice of pKa data sets 
depending on the reason for the pI calculation and make the Epk.dat file 
name specifiable by a new command line qualifier.

Hope this helps,

Peter Rice

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