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Option to fetch Genbank sequences in fasta format (Read 7542 times)
Mar 14th, 2013 at 5:49am

Peter   Offline
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When using "Fetch data from a remote database" and then selecting NCBI - UGENE fetches the sequence in "gb" format. It would be great if there was an option to fetch or save the sequence in "fasta" format.
 
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Reply #1 - Mar 14th, 2013 at 12:10pm

Yuriy Vaskin   Offline
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Hello!
Thanks for your question.

Any sequence which is loaded in UGENE can be converted in any supported format. If you load sequences with "File->Access remote database" then try "Export->Export sequences" in context menu of the sequence. You can select file format in the "Export" dialog. If you load sequences in Workflow Designer, then select output file format of an output element.
 
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Reply #2 - Mar 15th, 2013 at 1:15pm

Peter   Offline
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Dear Yuriy
Your workaround is good and certainly can solve the problem. However, it adds a couple of extra steps (Fetch -> export -> load)
As UGENE already contains the functionality to convert from *gb to *fasta - I was thinking it would be really helpful if this was done all in one go at the "fetch" stage.
thanks
 
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Reply #3 - Mar 15th, 2013 at 3:21pm

Konstantin Okonechnikov   Offline
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Hi Peter,
we plan to add an improved search interface to fetch data from NCBI, we will add option of the output format there:
https://ugene.unipro.ru/tracker/browse/UGENE-365
 
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Reply #4 - Mar 15th, 2013 at 4:05pm

Peter   Offline
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Hi Konstantin
This sounds great.
Being able to fluidly search for NCBI data and add it to an alignment would really take UGENE to a higher level.
You guys are really doing a great job!
regards
peter
 
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