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How can I use PSIPRED on UGENE without network? (Read 21559 times)
Jan 24th, 2013 at 7:07am

karin   Offline
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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 25th, 2013 at 4:36pm

Konstantin Okonechnikov   Offline
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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 25th, 2013 at 7:45pm

karin   Offline
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Hi, Konstantin.
Thank you for reply.

My words were not enough, sorry.

Konstantin Okonechnikov wrote on Jan 25th, 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 28th, 2013 at 4:12pm

Konstantin Okonechnikov   Offline
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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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