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Query Designer issue (Read 7074 times)

Feb 24^th, 2011 at 5:12pm

Agu Offline
Junior Member
(Argentinian)

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Posts: 63

Hi!
It's been too quiet during the last weeks (it means UGENE is getting better and better Wink

), but I have a bug to report.

I've been trying to identify automatically a couple of primers and to save as annotation the sequence in between (not including the primers).
First tried with the Search pattern, but there is no option for "match percentage" nor for direct or complementary strand (feature request). Then I used Smith-waterman algorithm and it worked. As they are supposed to be inside an ORF, I've tryied to use the ORF option but there is no way to disable the option "must terminate within region" (feature request). So far, I'm able to identify only the primers, but the bug comes when I change the way the second primer is annotated. The only way it works is if I set the orientation of the annotation as "any". If I put forward or backward it doesn't work. That is supposed to be the way it annotates the result, not the way it searches. Even more strange (it might be helpful to track the bug), that bad behaviour only happens when restricting the distances between primers (I've tried changing the type to "End to End", but it doesn't help).

I'm attaching the schema (working and not) and one sequence to use it.

Please, also check the phrase in parameters of the ORF option:
"Require init codon : Allow or not ORFs starting with any codon other than terminator" (ATG)

Cheers!

UGENE v. 1.9.1 and 1.9.2-dev (Ubuntu 10.10 and XP)

16.gb (16 KB | )

primers_working.uql (0 KB | )

primers_not_working.uql (0 KB | )

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Reply #1 - Feb 24^th, 2011 at 5:59pm

Agu Offline
Junior Member
(Argentinian)

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Posts: 63

Now moving to Workflow Designer.
I've just applied that schema to several files (really cool to see, very nice Smiley

), but the resulting files are a little messed up. The sequence is before the features ant there is a "//" in between. Please, have a look to the attached file with one of the generated files. The workflow is simple, "Read Sequence" (from a genbank file), apply the schema (the one sent in the previous post) and "Write genbank" to a new location (using the original annotations as well as the new generated by the schema. Very nice to be able to do that). . Is it possible to use the original name of the sequence for saving the new one?
Is there any log? The schema didn't work for one of them (it showed a window) but I don't know for which one (Otherwise I have to check manually).

Thanks.

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Reply #2 - Feb 24^th, 2011 at 7:35pm

Konstantin Okonechnikov Offline
Global Moderator

Posts: 173

Thanks for bug report!

The missing option in ORF Query will be added ASAP and the bug with "directed" search will be fixed. BTW did you try using original Primer query for your task?

Regarding workflow designer:

Quote:

The sequence is before the features ant there is a "//" in between. Please, have a look to the attached file with one of the generated files.

Did you use iterations in your workflow? If not, the resulting files will be merged into single genbank file. Genbank format supports having multiple sequences within it.

Quote:

Is it possible to use the original name of the sequence for saving the new one?

What do you mean by this? Do you want to rewrite original files with new content? Or do you want to keep original Genbank name (LOCUS and ACCSESSION) in result files?

Quote:

Is there any log? The schema didn't work for one of them (it showed a window) but I don't know for which one (Otherwise I have to check manually).

Check the Notifiaction message by clicking on "Memo" pic in the lower right corner of the screen (Check screenshot below). You can also add more detailed log levels in Application Settings

screenshot.gif (11 KB | )

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Reply #3 - Feb 24^th, 2011 at 8:06pm

Agu Offline
Junior Member
(Argentinian)

Gender:
Posts: 63

Thank you for your quick reply.

Quote:

BTW did you try using original Primer query for your task?

No, but because I'm trying to identify the region where this degenerated primers would anneal. So, I have the primers and I want to get the sequence of the product (but without primer sequences) from several sequences (~200). Now I was just annotating the position of these primers in all my sequences.

Quote:

Did you use iterations in your workflow? If not, the resulting files will be merged into single genbank file. Genbank format supports having multiple sequences within it.

No, I didn't. But the program says that if you don't need to change the parameters for each sequence, is better lo leave it without iterations. But still, I can set the program to save separate files instead of merging them in one genbank file even without iterations.

Quote:

Quote:

Is it possible to use the original name of the sequence for saving the new one?

What do you mean by this? Do you want to rewrite original files with new content? Or do you want to keep original Genbank name (LOCUS and ACCSESSION) in result files?

Sorry, not clear at all. I want to save a new file in another folder, but using the original file name (genomeA.gb).

Thanks for the log info, I didn't know that I could change the level of detail...

Another thing, the files generated with the workflow designer are not correct after the second sequence. The first one is OK, when UGENE starts to add the extension 001, 002, etc. to the file names, then they start to have the sequence before the features. I'm attaching one so you can have a look.

HPV_002.gb (18 KB | )

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Reply #4 - Feb 24^th, 2011 at 10:35pm

Mikhail Fursov Offline
YaBB Administrator

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Posts: 162

About working & not working query designer schemes: the issue is reproduced and will be fixed asap. We will report when updated snapshot is available.

---
UGENE team

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