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Hi, first of all, thank you very much for publishing this code!
I have a question about the fine tuned secondary structure prediction.
The predict_ss_rna.py script demonstrates how to use the fine t…
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Awhile ago I made a biopython issue mentioning a small bug I saw in the DNA nearest neighbor values. I caught that because I was using biopython's DNA nearest neighbor energies to bootstrap a library …
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Hi,
AptaSuite asks for using CapR for secondary structures prediction but this program calculates RNA folding. Do you have any suggestions how to involve DNA secondary structure prediction in AptaSu…
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- 3 virus grps
1. reference
2. redefining invertebrate rna virome data? Zika?
3. segmented, assembled (FMTV)
Zika (including raw), FMTV, study Holmes, Flaviref, Flavi all (deduplicate)
- q:…
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This could take as input an alignment of functional RNA molecule sequences, and output a matrix of mutual information scores for all pairs of positions in the alignment. That matrix could be plotted a…
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Work to be done section:
-Multi-sequence compare tools from the broad institute.
IGV: https://software.broadinstitute.org/software/igv/download
Some good command line softwares you will inevit…
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Hi there, can you provide your code for evaluate the performance of pseudo knot prediction?
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Project: ENCODE
So - we are working with a new High Throughput Sequencing Assay: icSHAPE, that captures RNA secondary structure.
NTR: "icSHAPE"
Editor preferred term: "icSHAPE"
Alternative…
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Hi:
Thank you very much for your data. The RNA tertiary structure of SARS-COV-2 is indeed an interesting topic, and the operation of FARFAR2 is really time-consuming. I'm a little confused about the…