[Bioperl-l] about pI prediction

[Frank]

Thanks very much!


Conrad Halling wrote:

> 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 it is out of date.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
>>
>