oligonucleotides
Design small interfering RNA and antisense oligonucleotide sequences against a transcript, and screen them for the failure modes specific to nucleic-acid drugs. Use this skill to tile a target transcript, apply positional and thermodynamic selection rules including duplex asymmetry and nearest-neighbour melting temperature, scan candidates for seed-region complementarity to off-target transcripts, and lay out a chemical modification pattern — gapmer architecture, 2'-O-methyl and 2'-MOE wings, locked nucleic acid, and phosphorothioate placement. Also trigger on siRNA, antisense oligonucleotide, ASO, gapmer, RNase H, seed region, duplex asymmetry, 2'-MOE, locked nucleic acid, phosphorothioate, or GalNAc conjugate.
- Version
- 1.0
- License
- MIT
- Compatibility
- Requires Python 3.10+ only. Sequence tiling, nearest-neighbour thermodynamics, and seed-match scanning are implemented in the standard library, so there is no install and no network access. Transcriptome-wide off-target scanning needs a local FASTA file that you supply; no reference sequence is bundled.
Pinned to revision f67572246d9b, so it is the text this page describes rather than whatever the author pushed since.
Pre-approved tools experimental
Experimental field. Support varies between clients, so this list is what the author declared, not what your client will enforce.
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Files
- skills/oligonucleotides/SKILL.md
- skills/oligonucleotides/references/chemical-modifications.md
- skills/oligonucleotides/references/delivery-and-safety.md
- skills/oligonucleotides/references/sirna-and-aso-design.md
- skills/oligonucleotides/scripts/_shared.py
- skills/oligonucleotides/scripts/chemistry_plan.py
- skills/oligonucleotides/scripts/offtarget_scan.py
- skills/oligonucleotides/scripts/oligo_design.py
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