UGENE Forum - How can I use PSIPRED on UGENE without network?

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How can I use PSIPRED on UGENE without network? (Read 22030 times)

Jan 24^th, 2013 at 7:07am

karin Offline
YaBB Newbies

Posts: 2

Hi, All.
I want to use psipred without network, i.e. stand-alone. It will be enable to use stand-alone with building local database by the original psipred manual. Embarrassed

Can I set the path to database on UGENE? or Must I rebuild UGENE?

environment: ugene 1.11.4 on Windows7 home premium SP1(64bit), memory 8GB.

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Reply #1 - Jan 25^th, 2013 at 4:36pm

Konstantin Okonechnikov Offline
Global Moderator

Posts: 173

Hi Karin,

Quote:

I want to use psipred without network, i.e. stand-alone. It will be enable to use stand-alone with building local database by the original psipred manual.

I am not sure what you mean by this. What is it exactly you would like to achieve? Is it weights database for neural network or is it a BlastP sequences database you wish to change?

Psipred is currently integrated into UGENE only on level of a single sequence, which means it predicts secondary structure without performing first BlastP alignment. We plan to add BLASTP alignment support for future versions.

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Reply #2 - Jan 25^th, 2013 at 7:45pm

karin Offline
YaBB Newbies

Posts: 2

Hi, Konstantin.
Thank you for reply.

My words were not enough, sorry.

Konstantin Okonechnikov wrote on Jan 25^th, 2013 at 4:36pm:

Psipred is currently integrated into UGENE only on level of a single sequence, which means it predicts secondary structure without performing first BlastP alignment. We plan to add BLASTP alignment support for future versions.

Original PSIPRED requires PSI-BLAST, some NCBI-tools and building local database if I used it without InterNet.

And I thought UGENE searched database through InterNet to predict 2nd structure with PSIPRED.

From your reply, it seems I can use PSIPRED if I have already fetched sequence data even when my machine is not connected to InterNet (my machine is stand-alone). Is it right?

Because my environment is not stable, and network connection is often down. And I wanted to predict 2nd structures without relying on the network system.

thank you.

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Reply #3 - Jan 28^th, 2013 at 4:12pm

Konstantin Okonechnikov Offline
Global Moderator

Posts: 173

Yes Karin, you're right, one can use the psipred in UGENE without having access to internet, although its prediction performance in general is lower without applying first the PSIBLAST search.

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