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https://forum.ugene.net/forum/YaBB.pl General Category >> Help and How-to >> BLAST output result in fasta formate https://forum.ugene.net/forum/YaBB.pl?num=1339844157 Message started by adnan on Jun 16^th, 2012 at 5:55pm

Title: BLAST output result in fasta formate
Post by adnan on Jun 16^th, 2012 at 5:55pm

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 :( ).

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

Title: Re: BLAST output result in fasta formate
Post by adnan on Jun 18^th, 2012 at 2:59pm

Any suggestions ?

Title: Re: BLAST output result in fasta formate
Post by Konstantin Okonechnikov on Jun 19^th, 2012 at 5:19am

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_annotations.html

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.

screenshot_fetch_seq.gif (30 KB | )

Title: Re: BLAST output result in fasta formate
Post by ILgix on Jan 17^th, 2013 at 6:28am

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!

Title: Re: BLAST output result in fasta formate
Post by Konstantin Okonechnikov on Jan 17^th, 2013 at 4:57pm

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

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.