phastCons
Conservation score from a two-state phylogenetic hidden Markov model fitted to a multiple alignment by maximum likelihood, from which conserved elements are predicted.
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. 9 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.
- phastCons100way_vertebrate (Cubuk et al. 2021) Configuration · configuration · 2 evaluations · 5 results
- phastCons20way_mammalian (Cubuk et al. 2021) Configuration · configuration · 2 evaluations · 6 results
- phastCons (mammalian) (Brandes et al. 2023 clinical benchmarks) Configuration · configuration · 4 evaluations · 8 results
- phastCons (primate) (Brandes et al. 2023 clinical benchmarks) Configuration · configuration · 4 evaluations · 8 results
- phastCons (vertebrate) (Brandes et al. 2023 clinical benchmarks) Configuration · configuration · 4 evaluations · 8 results
- phastCons100way_vertebrate rank score, dbNSFP 5.3.1a (Lee 2026) Configuration · configuration · 3 evaluations · 6 results
- phastCons17way_primate rank score, dbNSFP 5.3.1a (Lee 2026) Configuration · configuration · 3 evaluations · 6 results
- phastCons470way_mammalian rank score, dbNSFP 5.3.1a (Lee 2026) Configuration · configuration · 3 evaluations · 6 results
- phastCons (Livesey and Marsh 2025) Configuration · configuration · 6 evaluations · 7 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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Description Conservation score from a two-state phylogenetic hidden Markov model fitted to a multiple alignment by maximum likelihood, from which conserved elements are predicted. Individual claims | Abstract: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (phastCons) qa-descriptions-20261011-d-source-phastcons: abstractText Version: Europe PMC core record MED/16024819 (title and abstract), Genome Research 2005 | source checked ["automated-source-review","ai-assisted-source-review"] · 2026-10-11 Audit detailsApproved. Checked the 16 Pancotti-derived descriptions word for word against PMC8921618 section 2.2, ESM therm, RaSP and ELASPIC-2 against Chu 2024, ThermoMPNN against Dieckhaus 2024, and ABYSSAL and phyloP against their abstracts; all match. Licences on the new sources are supported by Europe PMC, the PMC XML and Crossref. Field: Claim: metadata-correction-8885be2ca23a67bc8a7f Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of a Europe PMC REST search response. These responses are not byte-stable (a later retrieval can differ in JSON key order); the title and abstractText fields are the evidence. |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- 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
- Abstract: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (phastCons) · Original source · Europe PMC core record MED/16024819 (title and abstract), Genome Research 2005
Technical metadata and extraction receipts
Stable ID: somatic-oncogenicity-20261009-method-phastcons
- areas
- dna-genomes
- contexts
- clinical_research
- method types
- specialist
- reported name
- phastCons
- 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
- configuration of: phastCons100way_vertebrate (Cubuk et al. 2021)
- configuration of: phastCons20way_mammalian (Cubuk et al. 2021)
- configuration of: phastCons (mammalian) (Brandes et al. 2023 clinical benchmarks)
- configuration of: phastCons (primate) (Brandes et al. 2023 clinical benchmarks)
- configuration of: phastCons (vertebrate) (Brandes et al. 2023 clinical benchmarks)
- subject: phastCons: description
- configuration of: phastCons100way_vertebrate rank score, dbNSFP 5.3.1a (Lee 2026)
- configuration of: phastCons17way_primate rank score, dbNSFP 5.3.1a (Lee 2026)
- configuration of: phastCons470way_mammalian rank score, dbNSFP 5.3.1a (Lee 2026)
- configuration of: phastCons (Livesey and Marsh 2025)