Method

FIMO

FIMO scans sequences for occurrences of supplied sequence motifs.

Sources (2)

https://meme-suite.org/meme/tools/fimo: page.html; https://meme-suite.org/meme/doc/copyright.html: copyright.html · Official FIMO page: motif input, sequence input, p-value threshold and strand options

0 evaluations · 0 metric rows

How it worksFIMO workflow

Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.

Sources (2)

At a glance

Model type

Statistical motif scanning procedure

Sources (2)

Inputs

DNA, RNA or protein sequences and motif matrices in the supported alphabet/formats.

Sources (2)

Outputs

Motif matches at sequence positions subject to the configured statistical threshold.

Sources (2)

Source reviewed · Automated source review, 2026-09-16. All specifications and missing details

Evaluations 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.

How it works

FIMO scans sequences for occurrences of supplied sequence motifs. Position-specific motif scanning with statistical match thresholds. The documented inputs are DNA, RNA or protein sequences and motif matrices in the supported alphabet/formats. The output consists of motif matches at sequence positions subject to the configured statistical threshold.

Sources (2)

Versions and reproducibility

MEME Suite FIMO; site snapshot pinned by retrieval time and hash. Input sequences and motif lengths, not a fixed language-model context.

Sources (2)

Strengths and limitations

Strengths supported by sources

Provides a simple motif-based reference whose supplied motif and background assumptions can be reported explicitly.
Sources (2)
https://meme-suite.org/meme/tools/fimo: page.html; https://meme-suite.org/meme/doc/copyright.html: copyright.html · Official FIMO page: motif input, sequence input, p-value threshold and strand options

Limitations and conditions

Motif matches do not establish molecular binding or regulation by themselves. Alphabet, strand and threshold choices affect the scan.
Sources (2)
https://meme-suite.org/meme/tools/fimo: page.html; https://meme-suite.org/meme/doc/copyright.html: copyright.html · Official FIMO page: motif input, sequence input, p-value threshold and strand options

Profile review details

Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied.

Stable record: discovery-model-fimo

Specifications

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.

Inputs, outputs and configuration
Property	Description and evidence
Model type	Statistical motif scanning procedure Sources (2) https://meme-suite.org/meme/tools/fimo: page.html; https://meme-suite.org/meme/doc/copyright.html: copyright.html · Official FIMO page: motif input, sequence input, p-value threshold and strand options
Architecture	Position-specific motif scanning with statistical match thresholds. Sources (2) https://meme-suite.org/meme/tools/fimo: page.html; https://meme-suite.org/meme/doc/copyright.html: copyright.html · Official FIMO page: motif input, sequence input, p-value threshold and strand options
Inputs	DNA, RNA or protein sequences and motif matrices in the supported alphabet/formats. Sources (2) https://meme-suite.org/meme/tools/fimo: page.html; https://meme-suite.org/meme/doc/copyright.html: copyright.html · Official FIMO page: motif input, sequence input, p-value threshold and strand options
Outputs	Motif matches at sequence positions subject to the configured statistical threshold. Sources (2) https://meme-suite.org/meme/tools/fimo: page.html; https://meme-suite.org/meme/doc/copyright.html: copyright.html · Official FIMO page: motif input, sequence input, p-value threshold and strand options
Parameters	Motif probabilities and scan settings; not a neural parameter count. Sources (2) https://meme-suite.org/meme/tools/fimo: page.html; https://meme-suite.org/meme/doc/copyright.html: copyright.html · Official FIMO page: motif input, sequence input, p-value threshold and strand options
Known versions	MEME Suite FIMO; site snapshot pinned by retrieval time and hash. Sources (2) https://meme-suite.org/meme/tools/fimo: page.html; https://meme-suite.org/meme/doc/copyright.html: copyright.html · Official FIMO page: motif input, sequence input, p-value threshold and strand options
Training data	Motifs are supplied by the user or a selected database. FIMO is the scanning procedure, not the motif-training method. Sources (2) https://meme-suite.org/meme/tools/fimo: page.html; https://meme-suite.org/meme/doc/copyright.html: copyright.html · Official FIMO page: motif input, sequence input, p-value threshold and strand options
Training cutoff	Inapplicable to neural pretraining; reference-database and input-data dates must be recorded for each run. · Not applicable Sources (2) https://meme-suite.org/meme/tools/fimo: page.html; https://meme-suite.org/meme/doc/copyright.html: copyright.html · Official FIMO page: motif input, sequence input, p-value threshold and strand options
Context limits	Input sequences and motif lengths, not a fixed language-model context. Sources (2) https://meme-suite.org/meme/tools/fimo: page.html; https://meme-suite.org/meme/doc/copyright.html: copyright.html · Official FIMO page: motif input, sequence input, p-value threshold and strand options
Weights licence	Inapplicable: supplied motif matrices replace neural weights. · Not applicable Sources (2) https://meme-suite.org/meme/tools/fimo: page.html; https://meme-suite.org/meme/doc/copyright.html: copyright.html · Official FIMO page: motif input, sequence input, p-value threshold and strand options
Access	Official project documentation and implementation: https://meme-suite.org/meme/tools/fimo Sources (2) https://meme-suite.org/meme/tools/fimo: page.html; https://meme-suite.org/meme/doc/copyright.html: copyright.html · Official FIMO page: motif input, sequence input, p-value threshold and strand options
Code licence	MEME Suite custom terms permit educational, research and non-profit use with notices retained; commercial use requires contacting UC San Diego for terms. Sources https://meme-suite.org/meme/doc/copyright.html: copyright.html · MEME Suite copyright notice: permission grant and commercial-use paragraph
Assumptions	Not extracted or verified for this record.

Applicable tests and references

Applicability is distinct from a completed evaluation.

DART-Eval · Proposed association

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.

39 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 summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	https://meme-suite.org/meme/doc/copyright.html: copyright.html Original source ↗ Official FIMO page: motif input, sequence input, p-value threshold and strand options Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Copyright 1994–2025; source snapshot 2026-09-16 Retrieved: 2026-09-16T20:41:37.711422+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `f54d004ea7c8e38222b76ffa4c04e072a204ccd948d41c3d46f55e36516b7262` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	https://meme-suite.org/meme/tools/fimo: page.html Original source ↗ Official FIMO page: motif input, sequence input, p-value threshold and strand options Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:46:20.892034+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `c0acb8f22d51b718d5c3a253e81b9882d804fa2aa153b6fcf3e826e22f085dd3` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps ["Motif matrices and sequence","Scan motif positions","Apply statistical threshold","Reported motif occurrences"] Individual claims	https://meme-suite.org/meme/doc/copyright.html: copyright.html Original source ↗ Official FIMO page: motif input, sequence input, p-value threshold and strand options Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Copyright 1994–2025; source snapshot 2026-09-16 Retrieved: 2026-09-16T20:41:37.711422+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `f54d004ea7c8e38222b76ffa4c04e072a204ccd948d41c3d46f55e36516b7262` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps ["Motif matrices and sequence","Scan motif positions","Apply statistical threshold","Reported motif occurrences"] Individual claims	https://meme-suite.org/meme/tools/fimo: page.html Original source ↗ Official FIMO page: motif input, sequence input, p-value threshold and strand options Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:46:20.892034+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `c0acb8f22d51b718d5c3a253e81b9882d804fa2aa153b6fcf3e826e22f085dd3` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title FIMO workflow Individual claims	https://meme-suite.org/meme/doc/copyright.html: copyright.html Original source ↗ Official FIMO page: motif input, sequence input, p-value threshold and strand options Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Copyright 1994–2025; source snapshot 2026-09-16 Retrieved: 2026-09-16T20:41:37.711422+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `f54d004ea7c8e38222b76ffa4c04e072a204ccd948d41c3d46f55e36516b7262` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title FIMO workflow Individual claims	https://meme-suite.org/meme/tools/fimo: page.html Original source ↗ Official FIMO page: motif input, sequence input, p-value threshold and strand options Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:46:20.892034+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `c0acb8f22d51b718d5c3a253e81b9882d804fa2aa153b6fcf3e826e22f085dd3` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Model type Statistical motif scanning procedure Individual claims	https://meme-suite.org/meme/doc/copyright.html: copyright.html Original source ↗ Official FIMO page: motif input, sequence input, p-value threshold and strand options Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Copyright 1994–2025; source snapshot 2026-09-16 Retrieved: 2026-09-16T20:41:37.711422+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `f54d004ea7c8e38222b76ffa4c04e072a204ccd948d41c3d46f55e36516b7262` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Model type Statistical motif scanning procedure Individual claims	https://meme-suite.org/meme/tools/fimo: page.html Original source ↗ Official FIMO page: motif input, sequence input, p-value threshold and strand options Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:46:20.892034+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `c0acb8f22d51b718d5c3a253e81b9882d804fa2aa153b6fcf3e826e22f085dd3` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Architecture Position-specific motif scanning with statistical match thresholds. Individual claims	https://meme-suite.org/meme/doc/copyright.html: copyright.html Original source ↗ Official FIMO page: motif input, sequence input, p-value threshold and strand options Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Copyright 1994–2025; source snapshot 2026-09-16 Retrieved: 2026-09-16T20:41:37.711422+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `f54d004ea7c8e38222b76ffa4c04e072a204ccd948d41c3d46f55e36516b7262` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Architecture Position-specific motif scanning with statistical match thresholds. Individual claims	https://meme-suite.org/meme/tools/fimo: page.html Original source ↗ Official FIMO page: motif input, sequence input, p-value threshold and strand options Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved page snapshot; no immutable publisher revision supplied Retrieved: 2026-09-16T19:46:20.892034+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `c0acb8f22d51b718d5c3a253e81b9882d804fa2aa153b6fcf3e826e22f085dd3` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

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Sources and history

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

3 source records and release history

meme official source · Original source · Not reported
https://meme-suite.org/meme/tools/fimo: page.html · Original source · Retrieved page snapshot; no immutable publisher revision supplied
https://meme-suite.org/meme/doc/copyright.html: copyright.html · Original source · Copyright 1994–2025; source snapshot 2026-09-16

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Technical metadata and extraction receipts

Stable ID: discovery-model-fimo

areas: genomics
access: official_source_linked
benchmark applicability: candidate; not evidence of a reported evaluation
candidate benchmark ids: discovery-benchmark-dart-eval
entity level: method
reported name: FIMO
version: Not reported
historical missing metadata: checkpoint: unextracted; code licence: unextracted; parameters: unextracted; training cutoff: unextracted; training data: unextracted; version: unextracted; weights licence: unextracted
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: model
entity classification: review date: 2026-09-17; rationale: The cited architecture/procedure describes an algorithm, representation recipe or software toolkit, rather than a single released learned biological model. Fitted models, selected reference databases and concrete runs remain separate configurations.; source ids: evidence-official-f0b17e30e69338b7762f; evidence-official-94c61d963d28fa3a8993; source locator: Official FIMO page: motif input, sequence input, p-value threshold and strand options; ambiguities: None recorded

Related records

applicable to: DART-Eval
model: Motif scanning

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