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BLAST output result in fasta formate (Read 10114 times)
Jun 16th, 2012 at 5:55pm

adnan   Offline
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Hello,

I recently started using Ugene and got a very basic question to ask (i tried searching in the forums but couldn't find it Sad ).

I used tblastn after downloading a genome and formatting it using formateDB.
It shows me now the graphical result and if i click on the blue diagram i can also see the sequence.

My question is how can i get all the blast hits in Fasta formate with hit identifier and sequence in one file ?

Many thanks
 
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Reply #1 - Jun 18th, 2012 at 2:59pm

adnan   Offline
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Any suggestions ?

 
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Reply #2 - Jun 19th, 2012 at 5:19am

Konstantin Okonechnikov   Offline
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Hi!  Do you want to get whole sequences or only the regions of annotated BLAST matches?
To get annotated regions one can use this feature:
http://ugene.unipro.ru/documentation/manual/plugins/dna_export/seq_of_selected_a...

It's also possible to fetch whole sequences by id from NCBI (will only work if the id of the sequence in the database corresponds to real Genbank id). See screenshot attached.


 
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Reply #3 - Jan 17th, 2013 at 6:28am

ILgix   Offline
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Dear Konstantin,
The link you provided doesnt work (File not found). Could you suggest once more, please, how to proceed when one want to have regions of annotated BLAST hits saved in FASTA format. I am using local DB and there is no such DB at the NCBI yet.
Thank you!
 
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Reply #4 - Jan 17th, 2013 at 4:57pm

Konstantin Okonechnikov   Offline
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Apparently manual structure has changed, here's fixed link:
http://ugene.unipro.ru/documentation/manual/sequence_view/sequence_manipulations...

For now it's not possible to get the full sequences of hits, only annotated regions.
Support for exporting the sequences will be added in next version. You can watch the progress here or comment on the issues here:
https://ugene.unipro.ru/tracker/browse/UGENE-1105
https://ugene.unipro.ru/tracker/browse/UGENE-1115

I'll update this thread when these features is availble from latest development snapshot.
 
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