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What genbank markers does UGENE use? (Read 9734 times)
Apr 8th, 2009 at 2:58pm

vigil   Offline
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Sorry if this is the wrong subforum for questions, couldn't figure it out.

I'm trying to write some data from a comma-separated values file into a genbank file (using python) so that I can see the info graphically.

My problem is UGENE doesn't want to display the files, which leads me to the question:

What characters/formating is neccessary for UGENE to recognize and display an annotation from a genbank file?

I guess this question has two parts,
what is required for recognition of a genbank file, and,
what is required for recognition of an individual feature/annotation to be displayed?

Again, I'm really happy with this program! Great work!

 
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Reply #1 - Apr 8th, 2009 at 4:10pm

vigil   Offline
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...a way around this problem, although it only makes me more confused:

1.Load the fasta file with DNA
2.Make an annotation and save it as a new file.
3.Write your own gb file.
4.Rename your gb file into the filename of the file you created in step 2.
 
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Reply #2 - Apr 8th, 2009 at 5:25pm

Mikhail Fursov   Offline
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UGENE recognizes Genbank files by checking LOCUS header string.

Could I ask you to  share genbank file you use so we can test it?
 

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Reply #3 - Apr 8th, 2009 at 7:24pm

vigil   Offline
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Sure. Here's a simple test file that I made.

When I try to load this, it gets highlighted in the objects window, but it doesn't show up in the (upper) sequence windows or (lower) annotation list window.

I can send my ugene file and the fasta dna seq I'm using if you like.

I CAN load this file by the procedure above, in this case saving a "fake" annotation as MyDocument_7.gb, then removing that file and renaming test.gb to MyDocument_7.gb.

I'm using 1.4.1 on Ubuntu 8.10
 

test.gb (0 KB | )
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Reply #4 - Apr 9th, 2009 at 2:03am

Mikhail Fursov   Offline
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Ok now I think I understand the problem.

Once you create an annotation  for your sequence UGENE creates an association between annotation table file and sequence file (GObjectRelation in code)

The association is stored in the active project file.

You can create this association manually for any sequence and annotation objects:

1) open a view for a sequence

2) add a file with annotations to the project

3) when the file with annotations is loaded drag&drop annotation table object to the sequence view

If sequence view contains multiple sequences you'll be prompted to select the sequence you want to add annotations to.

If the annotation object contains annotations with locations out of the sequence length range - UGENE will warn you about mapping error.

Once association is added, UGENE stores it in the project file without any affect to the sequence or annotation file.

Check if this work.
 

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Reply #5 - Apr 14th, 2009 at 2:20pm

vigil   Offline
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YES! That worked. Thankyou.
 
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