Hello.
I'm completely new to Ugene; please be patient with me.
I've been messing with Ugene's WorkFlow designer to do something that seems fairly easy, however, I'm unable to achieve it:

Read sequence --> Remote BLAST --> Get sequences by annotations --> Write genbank

Read sequence 2 (from genbank) --> Write FASTA

Read sequence 3 (from FASTA and sequence used in BLAST) --> Join sequences into alignment --> Align with Clustal (BLOSUM) --> Write Clustal

I want the sequences from the Genbank to have the same names when I write them to FASTA; instead, I get a sequence named "blast result 1"

What can I do?

Hi!
I see what you are trying to do, but it won't work that way.
The "Get Sequences By Annotations" element will return sequences of corresponding annotations. You provide BLAST results as annotations, therefore your initial sequence will be returned.
What you really need is an element that is called "Fetch sequences from annotations by id", which will allow to get each sequence from BLAST result.

Unfortunately such element doesn't exist yet :( We've created an issue of high priority:
https://ugene.unipro.ru/tracker/browse/UGENE-534
I will let you know in this thread, when it's resolved.

Meanwhile you can try do the same thing from Ugene GUI.
Take a lookt at the following thread:
http://ugene.unipro.ru/forum/YaBB.pl?num=1299946461
It's about phylogenetic analysis, but explains how to fetch sequences from BLAST results and make alignment out of them.

Thanks for your reply, Konstantin!

I checked my original post and found a mistake: I get as many  sequences as I request from BLAST (not one, as I wrote before).
However, that's irrelevant now because I could get the Ids the way I wanted with the thread you posted.

Thanks a lot