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https://forum.ugene.net/forum/YaBB.pl General Category >> Feature Requests >> Option to fetch Genbank sequences in fasta format https://forum.ugene.net/forum/YaBB.pl?num=1363214969 Message started by Peter on Mar 14^th, 2013 at 5:49am

Title: Option to fetch Genbank sequences in fasta format
Post by Peter on Mar 14^th, 2013 at 5:49am

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.

Title: Re: Option to fetch Genbank sequences in fasta format
Post by Yuriy Vaskin on Mar 14^th, 2013 at 12:10pm

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.

Title: Re: Option to fetch Genbank sequences in fasta format
Post by Peter on Mar 15^th, 2013 at 1:15pm

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

Title: Re: Option to fetch Genbank sequences in fasta format
Post by Konstantin Okonechnikov on Mar 15^th, 2013 at 3:21pm

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

Title: Re: Option to fetch Genbank sequences in fasta format
Post by Peter on Mar 15^th, 2013 at 4:05pm

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