Rhapsody
Machine-learning classifier of missense variant pathogenicity that combines sequence coevolution with features of protein structure and dynamics.
Results are recorded on linked configurations and versions of this method. Their settings and evaluations are kept separate below.
Results on linked records
This method has no results of its own in this release. One linked record has results. They are not assigned to the underlying method: each record keeps its own settings and evaluations, and its scores are on its own page.
- Rhapsody (Livesey and Marsh 2025) Configuration · configuration · 6 evaluations · 7 results
Overview
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Evidence
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Evidence table
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) · Original source · 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141
- Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Original source · PMC12016141 (published 2025-04-22; Genome Biol 26:104)
Technical metadata and extraction receipts
Stable ID: vep-lit-20261014-method-rhapsody
- areas
- dna-genomes; proteins-complexes
- contexts
- research; clinical_research
- method types
- supervised_machine_learning
- reported name
- Rhapsody
- entity level
- method
- source locator
- Supplementary Material 2, Table S2 row 72 ('Rhapsody')
- missing metadata
- version: reason: inapplicable; note: Family record; score versions are on configurations
- review
- reviewer: claude; reviewer note: Claude review agent; no human review claimed. Independent Claude (Opus 5.5) review agent, separate from the extraction agent that built this batch. Automated review only. Transcription, not reproduction.; reviewed at: 2026-10-14T15:30:00Z; artifact sha256: 1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70; retrieval url: https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-025-03575-w/MediaObjects/13059_2025_3575_MOESM2_ESM.xlsx; method: ai-assisted-source-review; scope-review; method note: Descriptive fields, identity links and missing-metadata reasons checked against the cited sources.; note: Checked; see the dated review for rulings on identity and method type.
- provenance note
- Livesey and Marsh 2025 class it as clinical-trained (trained on human variants with clinical labels, or using a predictor that was) and obtained its predictions from https://github.com/prody/rhapsody (Table S2).
Related records
- configuration of: Rhapsody (Livesey and Marsh 2025)