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https://forum.ugene.net/forum/YaBB.pl General Category >> Feature Requests >> Calculation of AA physico-chemical parameters (pI, mw, ...) https://forum.ugene.net/forum/YaBB.pl?num=1276011195 Message started by Sebastian on Jun 8^th, 2010 at 10:33pm

Title: Calculation of AA physico-chemical parameters (pI, mw, ...)
Post by Sebastian on Jun 8^th, 2010 at 10:33pm

Hi,

i would love to see a tool that could calculate/estimate pI, mw, extinction coefficient and AA-composition for AA sequences (like Protparam, ExPASy-Tools).
Hydrophobicity and hydrophilicity scales would also be nice :)

Title: Re: Calculation of AA physico-chemical parameters (pI, mw, ...)
Post by Ivan Efremov on Jun 10^th, 2010 at 11:57am

Hi Sebastian!

We will put this task on our TODO-list.

Maybe you can point out any open-source tool which we can integrate into UGENE to avoid implementing this algorithms from scratch?
It looks like expasy-guys do not provide the source of their applications.

Title: Re: Calculation of AA physico-chemical parameters (pI, mw, ...)
Post by Sebastian on Jun 10^th, 2010 at 4:28pm

Hi Ivan,

GENtle, released under GPL, can calculate pI, mw, hydrophobicity plot, etc.

Title: Re: Calculation of AA physico-chemical parameters (pI, mw, ...)
Post by Mikhail Fursov on Jun 10^th, 2010 at 8:55pm

Sebastian,

We will consider adding this option to UGENE. If feature implementation will look simple for us it will be added to the nearest release (July), otherwise we will put it into the plans for the August/September one.

Title: Re: Calculation of AA physico-chemical parameters (pI, mw, ...)
Post by Sebastian on Jun 10^th, 2010 at 9:58pm

Sounds great!