Support optimization using N1-methylpseudouridine with ViennaRNA #11

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joh16 wants to merge 2 commits into ChangLabSNU:main from joh16:feature/modified-bases

Contributor

joh16 commented May 20, 2024 •

edited

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Summary

This feature would be available after RNAFold(ViennaRNA) officially supports N1-methylpseudouridine
- Link to PR
Substitutes every uridine to N1-methylpseudouridine if command line flag --m1psi is provided
- Output sequence will contain 1 instead of U

Checklist

--folding-engine vienna with --m1psi working
--folding-engine vienna without --m1psi working
--folding-engine linearfold with --m1psi throws error (not supported)
--folding-engine linearfold without --m1psi working

Sample Result

Using Influenza_HA.fa from tutorial with 50 iterations
- Influenza_HA.zip

joh16 added 2 commits

May 20, 2024 17:57


          refactor: move ExecutionOptions to sequence_evaluator

74a1b1d


          feat: support m1psi flag

c26a3b2

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