Genomic element classification
Classify sequence windows as promoters, enhancers, exons, introns or other genomic elements.
- Benchmarks
- 6
- Protocols
- 8
- Coverage
- covered
Task atlas
58 nucleic-acid tasks, all connected to a benchmark.
Start from the biological question, then inspect its benchmarks, tracks, and protocol-aligned evaluations.
58 / 58 tasks
Promoter recognition
Recognize promoter sequence windows; promoter activity is counted separately under D3.
- Benchmarks
- 6
- Protocols
- 9
- Coverage
- covered
Enhancer recognition
Recognize enhancer sequence windows independent of quantitative activity.
- Benchmarks
- 5
- Protocols
- 10
- Coverage
- covered
TF binding-site prediction
Predict sequence-specific TF occupancy or binding sites.
- Benchmarks
- 7
- Protocols
- 0
- Coverage
- covered
Chromatin accessibility prediction
Predict cell-type-specific accessible chromatin from DNA sequence.
- Benchmarks
- 4
- Protocols
- 1
- Coverage
- covered
Histone-mark prediction
Predict histone-mark assay signal from sequence.
- Benchmarks
- 3
- Protocols
- 41
- Coverage
- covered
Splice-site prediction
Predict splice donor and acceptor positions.
- Benchmarks
- 8
- Protocols
- 18
- Coverage
- covered
Alternative splicing pattern prediction
Predict splice pattern or exon inclusion without a specific variant perturbation.
- Benchmarks
- 2
- Protocols
- 3
- Coverage
- covered
Polyadenylation-site prediction
Locate or rank polyadenylation sites.
- Benchmarks
- 1
- Protocols
- 3
- Coverage
- covered
ncRNA family classification
Assign ncRNA sequences to functional families.
- Benchmarks
- 7
- Protocols
- 2
- Coverage
- covered
RNA modification-site prediction
Predict modification status at candidate nucleotides.
- Benchmarks
- 3
- Protocols
- 1
- Coverage
- covered
RNA subcellular localization
Predict RNA localization from sequence or sequence-derived representations.
- Benchmarks
- 1
- Protocols
- 3
- Coverage
- covered
Sequence motif discovery
Recover interpretable motifs rather than only predictive scores.
- Benchmarks
- 1
- Protocols
- 0
- Coverage
- covered
RNA secondary-structure base-pair prediction
Predict base pairs or dot-bracket secondary structure.
- Benchmarks
- 5
- Protocols
- 40
- Coverage
- covered
RNA non-canonical base-pair prediction
Predict non-canonical pair identities and contacts.
- Benchmarks
- 1
- Protocols
- 0
- Coverage
- covered
RNA contact or distance-map prediction
Predict pairwise contacts or distances without full coordinates.
- Benchmarks
- 2
- Protocols
- 3
- Coverage
- covered
RNA 3D coordinate prediction
Predict RNA 3D coordinates from sequence and optional auxiliary inputs.
- Benchmarks
- 5
- Protocols
- 81
- Coverage
- covered
DNA shape prediction
Predict local DNA shape features.
- Benchmarks
- 1
- Protocols
- 0
- Coverage
- covered
3D genome contact prediction
Predict Hi-C-like contact patterns from long sequence.
- Benchmarks
- 2
- Protocols
- 1
- Coverage
- covered
RNA probing-reactivity prediction
Predict chemical probing reactivity.
- Benchmarks
- 5
- Protocols
- 21
- Coverage
- covered
RNA 3D model quality assessment
Rank or score candidate RNA 3D models.
- Benchmarks
- 6
- Protocols
- 0
- Coverage
- covered
RNA conformational ensemble prediction
Predict multiple conformers or a conformational distribution.
- Benchmarks
- 1
- Protocols
- 0
- Coverage
- covered
All-atom nucleic-acid complex structure prediction
Predict complexes containing DNA/RNA and proteins, ligands or other nucleic acids.
- Benchmarks
- 4
- Protocols
- 2
- Coverage
- covered
Promoter activity prediction
Predict quantitative promoter activity.
- Benchmarks
- 1
- Protocols
- 0
- Coverage
- covered
Enhancer activity prediction
Predict quantitative enhancer activity, often cell-type specific.
- Benchmarks
- 1
- Protocols
- 0
- Coverage
- covered
Sequence-to-gene-expression prediction
Predict expression from cis-regulatory DNA context.
- Benchmarks
- 2
- Protocols
- 1
- Coverage
- covered
mRNA stability or half-life prediction
Predict RNA abundance decay or half-life.
- Benchmarks
- 1
- Protocols
- 0
- Coverage
- covered
Translation efficiency or ribosome-load prediction
Predict mean ribosome loading or translation efficiency.
- Benchmarks
- 5
- Protocols
- 2
- Coverage
- covered
Alternative polyadenylation quantification
Predict relative poly(A) site usage.
- Benchmarks
- 2
- Protocols
- 1
- Coverage
- covered
RNA degradation and vaccine-stability prediction
Predict degradation-related measurements as in OpenVaccine.
- Benchmarks
- 2
- Protocols
- 10
- Coverage
- covered
Ribozyme activity prediction
Predict activity of ribozymes or catalytic RNAs.
- Benchmarks
- 1
- Protocols
- 0
- Coverage
- covered
Programmable RNA-switch function prediction
Predict function of toehold or related RNA switches.
- Benchmarks
- 1
- Protocols
- 1
- Coverage
- covered
Nucleic-acid fitness prediction
Predict assay-specific sequence fitness; mutation-specific RNA DMS is cross-referenced to D4.
- Benchmarks
- 2
- Protocols
- 2
- Coverage
- covered
Regulatory variant-effect prediction
Predict effects of non-coding variants on regulatory activity.
- Benchmarks
- 4
- Protocols
- 3
- Coverage
- covered
Expression variant-effect prediction
Predict variant-induced expression changes.
- Benchmarks
- 1
- Protocols
- 1
- Coverage
- covered
Splicing variant-effect prediction
Predict variant effects on splicing.
- Benchmarks
- 1
- Protocols
- 0
- Coverage
- covered
RNA-binding variant-effect prediction
Predict variant effects on RBP binding.
- Benchmarks
- 1
- Protocols
- 3
- Coverage
- covered
RNA DMS effect prediction
Predict mutation effects across RNA deep-mutational-scanning assays.
- Benchmarks
- 3
- Protocols
- 2
- Coverage
- covered
Molecular functional or pathogenic variant interpretation
Restricted here to molecular/functional challenges; patient-level diagnosis and PRS are excluded.
- Benchmarks
- 2
- Protocols
- 2
- Coverage
- covered
Evolutionary constraint and conservation prediction
Predict evolutionary constraint at nucleotide resolution.
- Benchmarks
- 1
- Protocols
- 0
- Coverage
- covered
TF–DNA binding specificity
Predict TF–DNA specificity across factors and sequences.
- Benchmarks
- 2
- Protocols
- 0
- Coverage
- covered
RNA–protein binding prediction
Predict RBP–RNA binding or binding sites.
- Benchmarks
- 3
- Protocols
- 23
- Coverage
- covered
RNA–RNA interaction prediction
Predict intermolecular RNA pairing or interaction.
- Benchmarks
- 1
- Protocols
- 7
- Coverage
- covered
RNA–small-molecule binding prediction
Predict whether and how strongly small molecules bind RNA.
- Benchmarks
- 5
- Protocols
- 0
- Coverage
- covered
Aptamer–target affinity prediction
Predict aptamer binding to proteins or other targets.
- Benchmarks
- 2
- Protocols
- 3
- Coverage
- covered
Nucleic-acid–protein interface or docking
Predict interaction interface or relative pose.
- Benchmarks
- 3
- Protocols
- 2
- Coverage
- covered
Nucleic-acid–small-molecule docking
Predict ligand poses in nucleic-acid targets.
- Benchmarks
- 3
- Protocols
- 0
- Coverage
- covered
Promoter sequence design
Design promoters for a target activity.
- Benchmarks
- 1
- Protocols
- 1
- Coverage
- covered
Enhancer or cis-regulatory design
Design cis-regulatory sequences for desired activity.
- Benchmarks
- 1
- Protocols
- 0
- Coverage
- covered
5′UTR and translation-control design
Design 5′UTRs for target translation.
- Benchmarks
- 1
- Protocols
- 0
- Coverage
- covered
mRNA coding and stability co-design
Design coding and untranslated regions jointly under therapeutic constraints.
- Benchmarks
- 1
- Protocols
- 0
- Coverage
- covered
RNA secondary-structure inverse folding
Generate sequences expected to fold into a target secondary structure.
- Benchmarks
- 1
- Protocols
- 1
- Coverage
- covered
RNA 3D-conditioned design
Generate sequences conditioned on a target tertiary structure.
- Benchmarks
- 2
- Protocols
- 0
- Coverage
- covered
Aptamer design
Generate aptamers for a chosen target.
- Benchmarks
- 1
- Protocols
- 0
- Coverage
- covered
CRISPR guide on-target design
Design guides for high on-target efficiency.
- Benchmarks
- 1
- Protocols
- 8
- Coverage
- covered
CRISPR guide off-target design
Design or rank guides to minimize off-target activity.
- Benchmarks
- 1
- Protocols
- 1
- Coverage
- covered
siRNA, ASO or shRNA design
Design therapeutic oligonucleotides; chemistries remain dataset-specific.
- Benchmarks
- 1
- Protocols
- 24
- Coverage
- covered
Programmable RNA-switch design
Design RNA switches or sensors with target response.
- Benchmarks
- 1
- Protocols
- 0
- Coverage
- covered
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