[Bioperl-l] about pI prediction

[Conrad Halling]

Frank,

The usual algorithm is to calculate the charge of the protein at a given 
pH, say 7.0, then iterate to converge to a pH where the calculated 
charge on the protein is zero.

In BioPerl, the calculation is performed by sub _calculate_iep() in 
Bio::Tools::pICalculator.

For the latest stable release of EMBOSS, the code for calculating the pI 
is in file EMBOSS-2.10/nucleus/embiep.c, function emblepPhConverge().

For a more lucid explanation of how the algorithm works, see page two of 
http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf.

-- Conrad


Frank wrote:
> Hi, Thanks all, I wil install them and do some analysis.    I did it via 
> net in http://us.expasy.org/tools/pi_tool.html before.  It is not so 
> convenient for mass data analysis.
> 
> Hi, Brian, do you have any idea about the principle of cacluate pI?  I 
> searched some references published in 1980s. I am not sure whether it is 
> out of date.
> 
> Frank
> 
> Brian Osborne wrote:
> 
>> Frank,
>>
>> I've used both Tools/pICalculator and Tools/SeqStats.
>>
>> Brian O.
>>
>> -----Original Message-----
>> From: bioperl-l-bounces at portal.open-bio.org
>> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Marc Logghe
>> Sent: Tuesday, May 17, 2005 4:09 PM
>> To: Frank; bioperl-l at portal.open-bio.org
>> Subject: RE: [Bioperl-l] about pI prediction
>>
>>
>> Hi Frank,
>>  
>>
>>> Dose anyone use the  bioperl module to predict pI and molecular 
>>> weight of a protein?   Thanks
>>>   
>>
>> Don't know of a pure BioPerl module to predict pI. You can use
>> Bio::Tools::SeqStats to get the molecular weight, though.
>> If you have EMBOSS installed, you can use the Bioperl wrapper to the
>> EMBOSS application 'pepstats' for both the pI and mol weight. Have a
>> look at the docs for Bio::Factory::EMBOSS.
>> However, you have to parse out the corresponding values. The EMBOSS
>> docs, including an example output you can find at
>> http://emboss.sourceforge.net/apps/pepstats.html
>> HTH,
>> Marc

-- 
Conrad Halling
conrad.halling at bifx.org