UGENE Forum - Calculation of AA physico-chemical parameters (pI, mw, ...)

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UGENE Forum › General Category › Feature Requests › Calculation of AA physico-chemical parameters (pI, mw, ...)

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Calculation of AA physico-chemical parameters (pI, mw, ...) (Read 8598 times)

Jun 8^th, 2010 at 10:33pm

Sebastian Offline
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Posts: 9

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

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Reply #1 - Jun 10^th, 2010 at 11:57am

Ivan Efremov Offline
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Novosibirsk

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Posts: 46

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.

UGENE team

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Reply #2 - Jun 10^th, 2010 at 4:28pm

Sebastian Offline
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Posts: 9

Hi Ivan,

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

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Reply #3 - Jun 10^th, 2010 at 8:55pm

Mikhail Fursov Offline
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Posts: 162

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.

---
UGENE team

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Reply #4 - Jun 10^th, 2010 at 9:58pm

Sebastian Offline
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Posts: 9

Sounds great!

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