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https://forum.ugene.net/forum/YaBB.pl General Category >> Bugs and Issues >> Splicing not properly displayed https://forum.ugene.net/forum/YaBB.pl?num=1295366155 Message started by Agu on Jan 18^th, 2011 at 10:55pm

Title: Splicing not properly displayed
Post by Agu on Jan 18^th, 2011 at 10:55pm

Hi. I found that UGENE is not picking the correct frame when a feature is made by joining different parts.
It's much easier to see it:

In this case is joining nt 7 to 31. A new codon is generated with nt 7, 31 and 32. Then it should continue in the third frame (not in the first as shown). So, to pick the proper frame it has to add the nt left behind (if any).

BTW, Ugene 1.9 is working great.

Do you still need the recommendation letter for the grant?

https://forum.ugene.net/forum/YaBB.pl?action=downloadfile;file=test_splicing.gb (0 KB | )

splicing_error.png (14 KB | )

Title: Re: Splicing not properly displayed
Post by Mikhail Fursov on Jan 19^th, 2011 at 12:25pm

Why do you think that frame is not correct here?

See, the base at position 31 is G, 32 -> A, 33 - G
The translation result is E, the acid letter is shown right above the middle of GAG.
The selection you've made starts from symbol 33, not 31.

Title: Re: Splicing not properly displayed
Post by Agu on Jan 19^th, 2011 at 3:27pm

You are right, but don't forget the extra nucleotide from the 5' piece. There you have 7 nts,
ATG AAA G _____________________GA GGC TGT//

After the splicing event, it will be:

ATG AAA GGA GGC TGT AGC//

Title: Re: Splicing not properly displayed
Post by Ivan Efremov on Jan 20^th, 2011 at 12:00pm

Hi Agu,
surely we will be glad to receive your recommendation.

Thank you!

Title: Re: Splicing not properly displayed
Post by Mikhail Fursov on Jan 20^th, 2011 at 4:28pm

Agu wrote on Jan 19^th, 2011 at 3:27pm:

Ok.

For some annotations with multiple regions: for example 'repeats', every new region of the annotated sequence is independent. So, in translation we must restart the frame for every region.

In your example you have annotation with multiple regions with the when second region depends on the first one.

The question is: how to differentiate them?

For example we can use the name (genbank feature's 'key') to set up this flag per annotation: 'gene', 'CDS' will get the flag ON.

Do you have any other idea on how to implement this feature?

Title: Re: Splicing not properly displayed
Post by Agu on Jan 20^th, 2011 at 10:23pm

I agree with you. Probably the best is to use the feature 'CDS' as a flag. I would add also the 'Orf' feature, although is not "official", it is useful sometimes to have something different to the CDS.
You should not use 'gene' as you can not use that with multiple regions in GenBank (It could be good to have that limitation in UGENE as well).
Thanks.

Title: Re: Splicing not properly displayed
Post by Mikhail Fursov on Feb 1^st, 2011 at 8:43pm

Fixed in 1.9.1 (to be released in a week)