SIFT
Position-specific scoring matrix built from sequence homology found by PSI-BLAST.
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. 14 linked records have 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.
- Concordant calls of Polyphen2_HVAR and SIFT and MutationTaster (Cubuk et al. 2021) Configuration · uses this model · 2 evaluations · 4 results
- MSC-SIFT-based (Cubuk et al. 2021) Configuration · uses this model · 2 evaluations · 5 results
- SIFT (Cubuk et al. 2021) Configuration · configuration · 2 evaluations · 5 results
- SIFT (Brandes et al. 2023 clinical benchmarks) Configuration · configuration · 4 evaluations · 8 results
- SIFT4G (Brandes et al. 2023 clinical benchmarks) Configuration · configuration · 4 evaluations · 8 results
- SIFT (Chen et al. 2020) Configuration · configuration · 4 evaluations · 20 results
- SIFT4G (Chen et al. 2020) Configuration · configuration · 4 evaluations · 20 results
- SIFT rank score, dbNSFP 5.3.1a (Lee 2026) Configuration · configuration · 3 evaluations · 6 results
- SIFT4G rank score, dbNSFP 5.3.1a (Lee 2026) Configuration · configuration · 3 evaluations · 6 results
- SIFT (Livesey and Marsh 2025) Configuration · configuration · 6 evaluations · 7 results
- SIFT4G (Livesey and Marsh 2025) Configuration · configuration · 6 evaluations · 7 results
- SIFT [ProteinGym 144fe22 clinical summary] Configuration · configuration · 1 evaluation · 1 result
- SIFT4G [ProteinGym 144fe22 clinical summary] Configuration · configuration · 1 evaluation · 1 result
- SIFT (Pejaver et al. 2022 calibration) Configuration · configuration · 3 evaluations · 10 results
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
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How it works, versions and access
Strengths, limitations and unresolved questions
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
3 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Description Position-specific scoring matrix built from sequence homology found by PSI-BLAST. Individual claims | Comprehensive assessment of computational algorithms in predicting cancer driver mutations somatic-oncogenicity-20261009-source-chen2020: Table 1, Summary of 33 computational algorithms included in this study Version: Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML | source checked ["automated-source-review","ai-assisted-source-review"] · 2026-10-11 Audit detailsApproved with two corrections, both applied: the MutFormer source licence is CC BY 4.0 per the arXiv abstract page, and the MetaRNN source locator now names the Background passage. Checked the 27 Chen 2020 descriptions row by row against Table 1 (PMC7033911) and spot-checked AlphaMissense, MisFit, popEVE, VARITY, MetaRNN, MutFormer and gMVP against their abstracts; accurate. Licences on the other new sources match Europe PMC. Field: Claim: metadata-correction-81fd050e577e43fe2973 Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Facets: method types1 values
| Comprehensive assessment of computational algorithms in predicting cancer driver mutations Chen et al. 2020 Table 1: SIFT uses a position-specific scoring matrix Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML | conflicting claim ["source-hash-verification","automated-source-review"] · 2026-10-12 Audit detailsCorrect the method type from specialist to conventional_pipeline (use-case baseline review 2026-10-12, table 2). Evidence from docs/reviews/use-cases/baselines-2026-10-12.md. Independent review 2026-10-12: approved. See docs/reviews/2026-10-12-method-type-corrections.md. Conflicting source claim: Field: Claim: metadata-correction-tags-20261012-1da5da9448288389b77c Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
Facets: method types1 values
| An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers Chen et al. 2020 Table 1: SIFT uses a position-specific scoring matrix Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: bioRxiv 2026.07.16.739080 v1, posted 2026-07-23; full-text HTML page | conflicting claim ["source-hash-verification","automated-source-review"] · 2026-10-12 Audit detailsCorrect the method type from specialist to conventional_pipeline (use-case baseline review 2026-10-12, table 2). Evidence from docs/reviews/use-cases/baselines-2026-10-12.md. Independent review 2026-10-12: approved. See docs/reviews/2026-10-12-method-type-corrections.md. Conflicting source claim: Field: Claim: metadata-correction-tags-20261012-1da5da9448288389b77c Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the full-text HTML page, which is mutable (site chrome, metrics). The PDF request returned HTTP 429. Extraction artifact SHA-256: |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- Comprehensive assessment of computational algorithms in predicting cancer driver mutations · Original source · Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML
- An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers · Original source · bioRxiv 2026.07.16.739080 v1, posted 2026-07-23; full-text HTML page
Technical metadata and extraction receipts
Stable ID: somatic-oncogenicity-20261009-method-sift
- areas
- dna-genomes
- contexts
- clinical_research
- method types
- conventional_pipeline
- reported name
- SIFT
- entity level
- method
- source locator
- Algorithm lists of the cited sources
- missing metadata
- version: reason: inapplicable; note: Family record; score sources are on configurations
Related records
- uses model: Concordant calls of Polyphen2_HVAR and SIFT and MutationTaster (Cubuk et al. 2021)
- uses model: MSC-SIFT-based (Cubuk et al. 2021)
- configuration of: SIFT (Cubuk et al. 2021)
- configuration of: SIFT (Brandes et al. 2023 clinical benchmarks)
- configuration of: SIFT4G (Brandes et al. 2023 clinical benchmarks)
- subject: SIFT: description
- subject: SIFT: facets.method_types
- configuration of: SIFT (Chen et al. 2020)
- configuration of: SIFT4G (Chen et al. 2020)
- configuration of: SIFT rank score, dbNSFP 5.3.1a (Lee 2026)
- configuration of: SIFT4G rank score, dbNSFP 5.3.1a (Lee 2026)
- configuration of: SIFT (Livesey and Marsh 2025)
- configuration of: SIFT4G (Livesey and Marsh 2025)
- configuration of: SIFT [ProteinGym 144fe22 clinical summary]
- configuration of: SIFT4G [ProteinGym 144fe22 clinical summary]
- configuration of: SIFT (Pejaver et al. 2022 calibration)