gkudla
commented
5 years ago Hi Jon,
We have run into similar issues in the past: some constraints never made it into the final structure. This could be some sort of issue with the hybrid-ss-min program, but we don't know exactly what causes it, except that it usually affects very short structure elements.
To check if the issue stands with comradesFold or hybrid-ss-min, I suggest you run hybrid-ss-min with a constraint file containing your single constraint and see what happens.
You should also double-check if positions 3998-4002 can in fact basepair with 5055-5059.
Please let me know once you've done these tests...
best, Greg
On Tue, Aug 27, 2019 at 3:27 PM PriceJon notifications@github.com wrote:
Hello,
I am hoping you can give some insight into an issue I am experiencing with comradesFold. I will try and give a minimal example. I have run comradesMakeContraints on a sequence that I wish to know the structure of. My .hyb files are sound and when plotting the chimeras there is evidence for a secondary structure. After running comradesMakeConstraints this structure is identified in the *ranked_interactions.txt file:
646 . 6556 RNA . . 5055 5059 . RNA . . 3998 4002 . count_total=5;count_last_clustering=5;two_way_merged=0;
This is then converted correctly into the *folding_constraints.txt file:
F 3998 5059 5
Then if I run comradesFold just with this 1 constraint it does not get included in the .accepted file and therefore it is not included in the final structure. But there are other contraints that have been identified by comradesMakeConstraints that are included. Have you noticed this behaviour before of some constraints not being included in any accepted files even though evidence has been found for them?
Any help / advice would be greatly appreciated.
Many thanks,
Jon
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PriceJon
Hello,
I am hoping you can give some insight into an issue I am experiencing with comradesFold. I will try and give a minimal example. I have run comradesMakeContraints on a sequence that I wish to know the structure of. My .hyb files are sound and when plotting the chimeras there is evidence for a secondary structure. After running comradesMakeConstraints this structure is identified in the *ranked_interactions.txt file:
646 . 6556 RNA . . 5055 5059 . RNA . . 3998 4002 . count_total=5;count_last_clustering=5;two_way_merged=0;
This is then converted correctly into the *folding_constraints.txt file:
F 3998 5059 5
Then if I run comradesFold just with this 1 constraint it does not get included in the .accepted file and therefore it is not included in the final structure. But there are other contraints that have been identified by comradesMakeConstraints that are included. Have you noticed this behaviour before of some constraints not being included in any accepted files even though evidence has been found for them?
Any help / advice would be greatly appreciated.
Many thanks,
Jon