Task

Bacterial promoter prediction

Bacterial promoter prediction evaluates whether a sequence model can distinguish promoter-labelled sequences under a specified dataset definition.

Sources

nbrg-ppcu/prokbert: README.md · ProkBERT README: promoter prediction task and fine-tuning examples

0 evaluations · 0 metric rows

At a glance

Inputs, training, access and other details

Explanatory profile: source reviewed · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Data, procedure and scoring
Property	Description and evidence
Entity type	Task guide; concrete protocol identities remain separate. Sources nbrg-ppcu/prokbert: README.md · ProkBERT README: promoter prediction task and fine-tuning examples
Datasets	No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. · Not applicable Sources nbrg-ppcu/prokbert: README.md · ProkBERT README: promoter prediction task and fine-tuning examples
Organisms	No shared organism population is defined at this guide level. Record it for each selected dataset. · Not applicable Sources nbrg-ppcu/prokbert: README.md · ProkBERT README: promoter prediction task and fine-tuning examples
Assays	No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. · Not applicable Sources nbrg-ppcu/prokbert: README.md · ProkBERT README: promoter prediction task and fine-tuning examples
Splits	No executable split is attached to this task identity. Use the selected protocol’s split manifest. · Not applicable Sources nbrg-ppcu/prokbert: README.md · ProkBERT README: promoter prediction task and fine-tuning examples
Allowed inputs	DNA sequences and promoter labels from a named reference dataset; organism and negative-set construction are protocol-specific. Sources nbrg-ppcu/prokbert: README.md · ProkBERT README: promoter prediction task and fine-tuning examples
Adaptation	No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. · Not applicable Sources nbrg-ppcu/prokbert: README.md · ProkBERT README: promoter prediction task and fine-tuning examples
Metrics	Classification metrics defined by the selected dataset and protocol; decision thresholds and class balance must be reported. Sources nbrg-ppcu/prokbert: README.md · ProkBERT README: promoter prediction task and fine-tuning examples
Baselines	Documented sequence classifiers or simple composition controls may be candidates; no measured baseline value is supplied by this guide. Sources nbrg-ppcu/prokbert: README.md · ProkBERT README: promoter prediction task and fine-tuning examples

How it works

How it worksConceptual evaluation workflow

Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol.

Sources

nbrg-ppcu/prokbert: README.md · ProkBERT README: promoter prediction task and fine-tuning examples

Choosing an evaluation

A concrete study must define what counts as a promoter, how negative examples are selected and which organisms or sequence groups are held out. Keep those decisions with the score. ProkBERT documents a promoter-prediction use case, but that implementation does not make every promoter dataset or split interchangeable.

Sources

nbrg-ppcu/prokbert: README.md · ProkBERT README: promoter prediction task and fine-tuning examples

Task scope

This is a task guide, not a single versioned benchmark protocol. The connected resources provide examples or concrete procedures. A candidate method or proposed control is not evidence that an evaluation has been completed.

Sources

nbrg-ppcu/prokbert: README.md · ProkBERT README: promoter prediction task and fine-tuning examples

Tested entities and results

Release 2026-09-17-d277315f7d76 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.

No evaluations linked in this release.

Papers and result coverage

Last literature check: 2026-09-17. Primary-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.

Paper or primary resource	Version	Reference
ProkBERT family: genomic language models for microbiome applications	PMC full-text XML snapshot PMC10810988 at retrieval; byte-pinned by SHA-256	Read source DOI: 10.3389/fmicb.2023.1331233

What is still missing

Broad bacterial promoter prediction includes other organisms and dataset constructions; one E. coli table is not a universal ranking.

Search and extraction details

broad task primary protocol linked

Searches

Open Problems single cell label projection benchmark v1.0.0 paper
CAPRI assessment rounds 46 54 protein docking results
GEARS predicting transcriptional outcomes multigene perturbations 2023
scVI scANVI reference mapping benchmark primary paper
Boltz-2 affinity benchmark paper
ESMFold monomer structure benchmark Science 2023
"ProkBERT" "paper" "2024"
"scPertEval"
ProkBERT family prokaryotic language models microbe paper
Probabilistic harmonization annotation single-cell transcriptomics scANVI Nature Methods 2021
Evolutionary-scale prediction atomic-level protein structure language model ESMFold Science Lin 2023
Towards Principled Evaluation Single-Cell Perturbation Prediction Models Schäfer 2026

Evidence locations

Sections 2.3 and 3.3
Table 3

Strengths and limitations

Strengths supported by sources

An explicit promoter-label task gives a sequence representation a measurable downstream endpoint.
Sources
nbrg-ppcu/prokbert: README.md · ProkBERT README: promoter prediction task and fine-tuning examples

Limitations and conditions

A classifier can exploit how negatives were sampled. Transfer to another organism or promoter definition needs its own evaluation.
Sources
nbrg-ppcu/prokbert: README.md · ProkBERT README: promoter prediction task and fine-tuning examples

Profile review details

Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol.

Stable record: catalog-task-microbial-promoters

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.

17 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
Property and statement	Original source and location	Review and provenance
Diagram caption Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol. Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: promoter prediction task and fine-tuning examples Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps ["Choose promoter labels and negatives","Fix organism or sequence holdout","Evaluate the defined classifier","Report classification and coverage"] Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: promoter prediction task and fine-tuning examples Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title Conceptual evaluation workflow Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: promoter prediction task and fine-tuning examples Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Entity type Task guide; concrete protocol identities remain separate. Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: promoter prediction task and fine-tuning examples Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Datasets No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: promoter prediction task and fine-tuning examples Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	inapplicable automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Organisms No shared organism population is defined at this guide level. Record it for each selected dataset. Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: promoter prediction task and fine-tuning examples Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	inapplicable automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Assays No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: promoter prediction task and fine-tuning examples Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	inapplicable automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Splits No executable split is attached to this task identity. Use the selected protocol’s split manifest. Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: promoter prediction task and fine-tuning examples Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	inapplicable automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Allowed inputs DNA sequences and promoter labels from a named reference dataset; organism and negative-set construction are protocol-specific. Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: promoter prediction task and fine-tuning examples Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	source checked automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.5.value` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Adaptation No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. Individual claims	nbrg-ppcu/prokbert: README.md Original source ↗ ProkBERT README: promoter prediction task and fine-tuning examples Version: 8670ae92b816cff158a0b85647a8dea122e251eb Retrieved: 2026-09-16T19:46:19.913949+00:00	inapplicable automated source review · 2026-09-16 Audit details Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: `attributes.profile.facts.6.value` Source artifact SHA-256: `29de39c6ad006ce704ab14240cfd97af93da411fb63ec89ebe499c2646928cfc` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

All evidence (CSV)All evidence (JSONL)How to read the evidence

Sources and history

Release 2026-09-17-d277315f7d76 · Record review: discovered

4 source records and release history

ProkBERT official resource · Original source · Not reported
Evo 2 official resource · Original source · Not reported
ProkBERT family: genomic language models for microbiome applications · Original source · PMC full-text XML snapshot PMC10810988 at retrieval; byte-pinned by SHA-256
nbrg-ppcu/prokbert: README.md · Original source · 8670ae92b816cff158a0b85647a8dea122e251eb

Download this release

Technical metadata and extraction receipts

Stable ID: catalog-task-microbial-promoters

areas: microbes-communities
entity level: task
version: Not reported
task: Bacterial promoter prediction
scope note: Classify promoter activity from microbial DNA sequence.
benchmark research: review date: 2026-09-17; status: broad_task_primary_protocol_linked; primary sources: expansion-p3-prokbert; inspected locators: Sections 2.3 and 3.3; Table 3; searched queries: Open Problems single cell label projection benchmark v1.0.0 paper; CAPRI assessment rounds 46 54 protein docking results; GEARS predicting transcriptional outcomes multigene perturbations 2023; scVI scANVI reference mapping benchmark primary paper; Boltz-2 affinity benchmark paper; ESMFold monomer structure benchmark Science 2023; "ProkBERT" "paper" "2024"; "scPertEval"; ProkBERT family prokaryotic language models microbe paper; Probabilistic harmonization annotation single-cell transcriptomics scANVI Nature Methods 2021; Evolutionary-scale prediction atomic-level protein structure language model ESMFold Science Lin 2023; Towards Principled Evaluation Single-Cell Perturbation Prediction Models Schäfer 2026; gaps: Broad bacterial promoter prediction includes other organisms and dataset constructions; one E. coli table is not a universal ranking.; claim scope: Primary-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.
historical missing metadata: protocol version: not_yet_extracted
metadata review scope: historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
legacy kinds: benchmark
entity classification: review date: 2026-09-17; rationale: This record identifies the biological prediction question or a suite-specific task, rather than a uniquely fixed evaluated procedure. Preserve its task identity and leave split, model adaptation and scoring details on linked protocols/evaluations.; source ids: evidence-official-2efbfaba5a1c09f4f7fa; source locator: ProkBERT README: promoter prediction task and fine-tuning examples; ambiguities: None recorded

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