Sequence Scoring

Genomic Intelligence

Genomic Intelligence serves transformer DNA language models that score regulatory function directly from sequence. This toolkit exposes seven tools over its /v1 REST API: gi-promoter (promoter regions), gi-splice (donor and acceptor sites), gi-enhancer (enhancer activity), gi-chromatin (chromatin state), gi-annotation (de-novo transcripts), gi-expression (expression from a TSS window), and gi-find-genes-and-predict-expression (both, in one call). Inference runs on the vendor’s service, so no weights are downloaded and no GPU is needed.

License: Genomic Intelligence is a client for the hosted Genomic Intelligence API; inference runs on the vendor’s service under Genomic Intelligence Terms of Service. Submitted sequences are transmitted to Genomic Intelligence. Attribution to Genomic Intelligence is required when results are redistributed. The client wrapper code is MIT-licensed. Please refer to the service terms for full terms. Research and development use. Not for clinical or diagnostic decisions.

Proto is not affiliated with Genomic Intelligence. This toolkit is open source and builds on the implementation produced by this organization. Product names, logos, and trademarks are the property of their respective owners.

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genomicintelligence.ai

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@misc{genomic_intelligence_api,
  title        = {Genomic Intelligence: DNA sequence analysis API},
  author       = {{Genomic Intelligence}},
  year         = {2026},
  howpublished = {\url{https://docs.genomicintelligence.ai}},
  note         = {Hosted transformer DNA language models for promoter, splice, enhancer,
                  chromatin, expression and gene-annotation prediction. Accessed 2026-08-19.}
}

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evo-design/proto-tools/proto_tools/tools/sequence_scoring/genomic_intelligence

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Developed byGenomic Intelligence

Function	Description
`run_gi_annotation()`	Find genes and transcripts de novo in raw DNA via the hosted Genomic Intelligence API	Docs Source
`run_gi_chromatin()`	Predict chromatin accessibility, TF occupancy and histone marks via the hosted Genomic Intelligen…	Docs Source
`run_gi_enhancer()`	Predict developmental and housekeeping enhancer activity via the hosted Genomic Intelligence API	Docs Source
`run_gi_expression()`	Predict gene expression from a TSS-centred window via the hosted Genomic Intelligence API	Docs Source
`run_gi_find_genes_and_predict_expression()`	Annotate genes in a locus and predict expression for each, via the hosted Genomic Intelligence API	Docs Source
`run_gi_promoter()`	Predict promoter regions in DNA via the hosted Genomic Intelligence API	Docs Source
`run_gi_splice()`	Predict splice donor and acceptor sites via the hosted Genomic Intelligence API	Docs Source

This toolkit was developed by Genomic Intelligence.

Background

Sequence-to-function models predict regulatory readouts from DNA alone, without an assay. Genomic Intelligence hosts a family of them behind one API: promoter and enhancer classifiers, a splice-site model, a chromatin-state panel spanning accessibility, transcription-factor occupancy and histone marks, a structure-aware gene finder, and an expression model conditioned on experimental context. Each task is a separate published operation with its own request schema and its own minimum input length, so bounds are per task rather than global. Every tool here is a thin HTTPS client. A request carries the sequence and the task’s options; the service resolves which model version to run, so model is left unset by default and the alternatives are enumerable through GET /v1/tasks/{task}/models. Delivery is a per-request choice on every endpoint: omitting the Prefer header returns the result synchronously, while respond_async returns a job id to poll. Coordinates in tool outputs are 0-based with exclusive ends, following the genomics interval convention used elsewhere in sequence_scoring rather than the 1-based residue numbering used across the rest of proto-tools.

Learning Resources

Genomic Intelligence API reference (Genomic Intelligence) - endpoint documentation, worked examples, and the per-task input bounds.
OpenAPI document (Genomic Intelligence) - the machine-readable contract: every field, bound, enum and status code.

Tools

GI Promoter (`gi-promoter`)

Slides a promoter classifier across the sequence and returns the windows called as promoters, the contiguous regions they form, and the per-window probabilities behind both.

API Reference

Source

Input: GIPromoterInput

List[GISequence]

required

Sequences to score. A bare DNA string is accepted and coerced. Each must be at least 300 bp, the endpoint’s published floor.

Show GISequence

string

required

DNA sequence. Length bounds are per task and are checked against the endpoint’s published values before any request.

string

default:"sequence"

Label echoed back in the response, useful for correlating results in a batch.

Source

Config: GIPromoterConfig

number

default:"0.5"

Probability above which a window is called a promoter. Applied server-side.

integer

default:"0"

Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). True is coerced to 1 and False to 0.

string

default:"cpu"

Device to run the tool on.

integer

default:"3600"

Maximum execution time in seconds. None waits indefinitely.

integer

Random seed. When set, tools run reproducibly up to small GPU float noise (see BaseToolOutput.approx_equal), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

string

Bearer key for the hosted API. Defaults to the GI_API_KEY environment variable.

string

Model identifier. Leave unset: the service resolves the current default for the task.

boolean

default:"False"

Request 202 + polling instead of a synchronous 200. A per-request delivery choice available on every endpoint.

number

default:"1800.0"

Wall-clock cap on the async wait.

Source

Output: GIPromoterOutput

List[GIPromoterResult]

required

One result per submitted sequence, in the order submitted.

Show GIPromoterResult

string

required

Label supplied with the sequence.

integer

required

Length of the submitted sequence in base pairs.

integer

required

Number of windows that cleared the threshold.

integer

required

Number of windows scored.

number

Highest window probability, or None when no window was scored.

List[PromoterRegion]

Regions called as promoters.

List[PromoterWindow]

Every scored window.

GIRequestMeta

required

Provenance for the call.

Applications

Use this to locate transcription start regions in unannotated sequence, or to score designed constructs for promoter strength inside an optimization loop. The per-window probabilities make it usable as a fitness signal rather than only a binary call.

Usage Tips

Minimum input is 300 bp. This is a task floor published on the endpoint’s request schema, so selecting a different model does not lower it.
Windows shorter than the model’s context are padded. A short sequence still scores, but the model sees padding; compare against the model’s context window when interpreting a marginal call.
threshold is applied server-side. Lowering it returns more regions without re-running inference.

GI Splice Sites (`gi-splice`)

Predicts splice donor and acceptor sites, returning each site’s span, class and score together with per-class counts.

API Reference

Source

Input: GISpliceInput

List[GISequence]

required

Sequences to score, in transcript orientation. A bare DNA string is accepted and coerced. Each must be at least 100 bp, the endpoint’s published floor.

Show GISequence

string

required

DNA sequence. Length bounds are per task and are checked against the endpoint’s published values before any request.

string

default:"sequence"

Label echoed back in the response, useful for correlating results in a batch.

Source

Config: GISpliceConfig

number

default:"0.5"

Score above which a position is reported as a site. Values at or near zero return every scored position and produce very large responses; the default is a good working value.

array

Restrict the reported site classes. Leave unset to report both.

integer

default:"0"

Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). True is coerced to 1 and False to 0.

string

default:"cpu"

Device to run the tool on.

integer

default:"3600"

Maximum execution time in seconds. None waits indefinitely.

integer

string

Bearer key for the hosted API. Defaults to the GI_API_KEY environment variable.

string

Model identifier. Leave unset: the service resolves the current default for the task.

boolean

default:"False"

Request 202 + polling instead of a synchronous 200. A per-request delivery choice available on every endpoint.

number

default:"1800.0"

Wall-clock cap on the async wait.

Source

Output: GISpliceOutput

List[GISpliceResult]

required

One result per submitted sequence, in the order submitted.

Show GISpliceResult

string

required

Label supplied with the sequence.

integer

required

Length of the submitted sequence in base pairs.

integer

required

Number of sites reported.

integer

required

Number of donor sites reported.

integer

required

Number of acceptor sites reported.

List[SpliceSite]

The reported sites.

GIRequestMeta

required

Provenance for the call.

Applications

Use this to locate exon boundaries in unannotated transcripts, to check whether a designed edit creates or destroys a splice site, or to screen variants for splice disruption.

Usage Tips

Submit transcript orientation. The model is strand-specific, and the wrong strand does not fail loudly: it returns sites at different positions, frequently at high confidence. No score or count identifies a mis-oriented submission after the fact, so reverse-complement minus-strand genes before calling.
A site’s start/end is a token span, not the junction base. It bounds one variable-width tokenizer token — 4–10 bp across the sequences measured so far — and the exon/intron boundary lies somewhere inside it. Locate a boundary to within the span; do not reduce the pair to a single base position, and do not intersect it against reference annotation as though it were one.
Minimum input is 100 bp.
Very low thresholds return every scored position. The response grows accordingly; the default is a working value.

GI Enhancer Activity (`gi-enhancer`)

Scores developmental and housekeeping enhancer activity per window, following the STARR-seq split between the two programmes.

API Reference

Source

Input: GIEnhancerInput

List[GISequence]

required

Sequences to score. A bare DNA string is accepted and coerced. Each must be at least 50 bp, the endpoint’s published floor.

Show GISequence

string

required

DNA sequence. Length bounds are per task and are checked against the endpoint’s published values before any request.

string

default:"sequence"

Label echoed back in the response, useful for correlating results in a batch.

Source

Config: GIEnhancerConfig

integer

default:"0"

Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). True is coerced to 1 and False to 0.

string

default:"cpu"

Device to run the tool on.

integer

default:"3600"

Maximum execution time in seconds. None waits indefinitely.

integer

string

Bearer key for the hosted API. Defaults to the GI_API_KEY environment variable.

string

Model identifier. Leave unset: the service resolves the current default for the task.

boolean

default:"False"

Request 202 + polling instead of a synchronous 200. A per-request delivery choice available on every endpoint.

number

default:"1800.0"

Wall-clock cap on the async wait.

Source

Output: GIEnhancerOutput

List[GIEnhancerResult]

required

One result per submitted sequence, in the order submitted.

Show GIEnhancerResult

string

required

Label supplied with the sequence.

integer

required

Length of the submitted sequence in base pairs.

integer

required

Number of windows scored.

number

Highest developmental score.

number

Highest housekeeping score.

List[EnhancerWindow]

Every scored window.

GIRequestMeta

required

Provenance for the call.

Applications

Use this to rank candidate enhancers, or as a dual-objective fitness function when designing regulatory elements that favour one programme over the other.

Usage Tips

Minimum input is 50 bp, the lowest floor in the toolkit.
The developmental/housekeeping split is a Drosophila assay definition. Read the two scores as relative activity within a comparison rather than as calibrated cross-species values.
The endpoint declares no task-specific options. Only the shared configuration applies.

GI Chromatin State (`gi-chromatin`)

Scores each window against a large panel of chromatin assays across many cell types, returning how many calls clear the threshold, per window and per assay category.

API Reference

Source

Input: GIChromatinInput

List[GISequence]

required

Sequences to score. A bare DNA string is accepted and coerced. Each must be at least 200 bp, the endpoint’s published floor.

Show GISequence

string

required

DNA sequence. Length bounds are per task and are checked against the endpoint’s published values before any request.

string

default:"sequence"

Label echoed back in the response, useful for correlating results in a batch.

Source

Config: GIChromatinConfig

number

default:"0.5"

Probability above which an assay call is reported. The panel is large, so lowering this materially increases response size.

integer

default:"0"

Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). True is coerced to 1 and False to 0.

string

default:"cpu"

Device to run the tool on.

integer

default:"3600"

Maximum execution time in seconds. None waits indefinitely.

integer

string

Bearer key for the hosted API. Defaults to the GI_API_KEY environment variable.

string

Model identifier. Leave unset: the service resolves the current default for the task.

boolean

default:"False"

Request 202 + polling instead of a synchronous 200. A per-request delivery choice available on every endpoint.

number

default:"1800.0"

Wall-clock cap on the async wait.

Source

Output: GIChromatinOutput

List[GIChromatinResult]

required

One result per submitted sequence, in the order submitted.

Show GIChromatinResult

string

required

Label supplied with the sequence.

integer

required

Length of the submitted sequence in base pairs.

integer

required

Number of windows scored.

integer

required

Assay calls above the threshold, summed.

Dict[string, integer]

Calls per assay category.

List[ChromatinWindow]

Per-window call counts.

GIRequestMeta

required

Provenance for the call.

Applications

Use this to ask whether a sequence looks accessible, bound, or marked in a given cellular context, and to compare designed variants against a natural reference across many assays at once.

Usage Tips

Minimum input is 200 bp.
The panel is large. Lowering threshold materially increases the size of the response the service returns.
Calls span many cell types and assays. The tool reports totals and per-category counts rather than the individual calls, so a high count is not evidence about any one cellular context.

GI Gene Annotation (`gi-annotation`)

Finds transcripts de novo in raw sequence with no reference, returning each transcript’s bounds, strand, confidence score, and TSS and poly(A) positions.

API Reference

Source

Input: GIAnnotationInput

List[GISequence]

required

Sequences to annotate. A bare DNA string is accepted and coerced. Each must be at least 1,000 bp, the endpoint’s published floor.

Show GISequence

string

required

DNA sequence. Length bounds are per task and are checked against the endpoint’s published values before any request.

string

default:"sequence"

Label echoed back in the response, useful for correlating results in a batch.

Source

Config: GIAnnotationConfig

integer

Server-side batching hint. Leave unset for the service default.

boolean

Also scan the reverse complement. Detection already finds genes on either strand, so this changes the reported orientation rather than whether genes are found.

integer

default:"0"

Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). True is coerced to 1 and False to 0.

string

default:"cpu"

Device to run the tool on.

integer

default:"3600"

Maximum execution time in seconds. None waits indefinitely.

integer

string

Bearer key for the hosted API. Defaults to the GI_API_KEY environment variable.

string

Model identifier. Leave unset: the service resolves the current default for the task.

boolean

default:"False"

Request 202 + polling instead of a synchronous 200. A per-request delivery choice available on every endpoint.

number

default:"1800.0"

Wall-clock cap on the async wait.

Source

Output: GIAnnotationOutput

List[GIAnnotationResult]

required

One result per submitted sequence, in the order submitted.

Show GIAnnotationResult

string

required

Label supplied with the sequence.

integer

required

Length of the submitted sequence in base pairs.

integer

required

Number of transcripts found.

integer

Transcripts on the submitted orientation.

integer

Transcripts on the opposite orientation.

List[Transcript]

The transcripts found.

GIRequestMeta

required

Provenance for the call.

Applications

Use this to annotate assembled contigs or synthetic constructs where no reference annotation exists, and to supply TSS positions to gi-expression when they are not known in advance.

Usage Tips

Minimum input is 1,000 bp, the highest floor apart from expression.
Detection is strand-insensitive. Genes on either strand are found from a single submission, and the reported strand is relative to the sequence as submitted.
This is the slowest task. Setting respond_async returns a job id and polls it, which avoids holding a long request open. That is a latency preference, not a requirement.

GI Gene Expression (`gi-expression`)

Predicts expression as log(TPM+1) from a single 9,198 bp window centred on a transcription start site, conditioned on a free-text description of the experimental context.

API Reference

Source

Input: GIExpressionInput

List[ExpressionSequence]

required

Loci to score, each carrying its own TSS offset where needed.

Show ExpressionSequence

string

required

Either exactly 9,198 bp centred on the TSS, or a longer locus paired with tss_index.

string

default:"sequence"

Label echoed back in the response.

integer

0-based TSS offset into the whitespace-stripped sequence. Required unless the sequence is exactly 9,198 bp, where it defaults to the midpoint. Must satisfy 4599 <= tss_index <= len(sequence) - 4599.

Source

Config: GIExpressionConfig

string

Experimental context the model is conditioned on — cell type, assay, conditions. Required. This is model input, not a

integer

default:"0"

Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). True is coerced to 1 and False to 0.

string

default:"cpu"

Device to run the tool on.

integer

default:"3600"

Maximum execution time in seconds. None waits indefinitely.

integer

string

Bearer key for the hosted API. Defaults to the GI_API_KEY environment variable.

string

Model identifier. Leave unset: the service resolves the current default for the task.

boolean

default:"False"

Request 202 + polling instead of a synchronous 200. A per-request delivery choice available on every endpoint.

number

default:"1800.0"

Wall-clock cap on the async wait.

Source

Output: GIExpressionOutput

List[ExpressionPrediction]

required

One result per submitted locus, in the order submitted.

Show ExpressionPrediction

string

required

Label supplied with the sequence.

integer

required

Length of the submitted sequence in base pairs, whitespace-stripped. Read from meta, not from data.input: the echo carries a field of the same name holding the 9,198 bp window instead, and only meta is in the published schema.

number

Predicted log(TPM+1).

number

Predicted TPM.

integer

TSS offset the service applied.

array

Window the service actually scored, as [start, end) in the submitted sequence.

GIRequestMeta

required

Provenance for the call.

Applications

Use this to estimate the transcriptional output of a locus or a designed promoter under a stated cellular context, and as the objective in an expression-maximizing or expression-matching design loop.

Usage Tips

The window is exact. Submit exactly 9,198 bp centred on the TSS, or a longer locus plus tss_index and let the service cut it. Under-length input is rejected rather than padded.
description is conditioning text, not a label. It is fed to the model, so rewording it changes the prediction. Hold it fixed across runs you intend to compare.
An in-range but wrong tss_index still scores. It simply scores a different window, so the tool reads the applied window back from the response rather than assuming the request’s.
The sequence is never reverse-complemented. Submit minus-strand genes in transcript orientation.

GI Find Genes and Predict Expression (`gi-find-genes-and-predict-expression`)

Runs annotation over a locus and then predicts expression for every gene found, centring each window on that gene’s own TSS.

API Reference

Source

Input: GIFindGenesInput

List[GISequence]

required

Loci to process. A bare DNA string is accepted and coerced. Each must be at least 1,000 bp, the endpoint’s published floor.

Show GISequence

string

required

DNA sequence. Length bounds are per task and are checked against the endpoint’s published values before any request.

string

default:"sequence"

Label echoed back in the response, useful for correlating results in a batch.

Source

Config: GIFindGenesConfig

string

Experimental context applied to every gene found. Conditioning text fed to the expression model, so its wording changes the predictions. The service requires it even though the published schema marks it optional.

string

Override the annotation stage’s model. Leave unset.

string

Override the expression stage’s model. Leave unset.

integer

default:"0"

Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). True is coerced to 1 and False to 0.

string

default:"cpu"

Device to run the tool on.

integer

default:"3600"

Maximum execution time in seconds. None waits indefinitely.

integer

string

Bearer key for the hosted API. Defaults to the GI_API_KEY environment variable.

string

Model identifier. Leave unset: the service resolves the current default for the task.

boolean

default:"False"

Request 202 + polling instead of a synchronous 200. A per-request delivery choice available on every endpoint.

number

default:"1800.0"

Wall-clock cap on the async wait.

Source

Output: GIFindGenesOutput

List[GIFindGenesResult]

required

One result per submitted locus, in the order submitted.

Show GIFindGenesResult

string

required

Label supplied with the sequence.

integer

required

Length of the submitted sequence in base pairs.

integer

required

Genes the annotation stage reported.

integer

required

Genes expression was predicted for.

List[GenePrediction]

One record per gene found.

GIRequestMeta

required

Provenance for the call.

Applications

Use this when the TSS positions are not known in advance — annotating and scoring a whole locus in one call — rather than chaining gi-annotation into gi-expression yourself.

Usage Tips

Minimum input is 1,000 bp, and the ceiling is the endpoint’s own 500,000 bp, which is not the expression model’s window.
This is the only endpoint with a delivery rule. A synchronous request above 50,000 bp is refused; the tool switches to polling automatically.
Genes too close to a sequence boundary are skipped, with the reason reported, because there is not enough flanking sequence for a full window.
JSON only. Unlike the predict endpoints, it declares no text output format.

Toolkit Notes

These apply to every tool in this toolkit (gi-promoter, gi-splice, gi-enhancer, gi-chromatin, gi-annotation, gi-expression, gi-find-genes-and-predict-expression).

Requires network access and an API key. Every tool calls the hosted Genomic Intelligence API. None runs offline, and no weights are downloaded. Set GI_API_KEY, or pass gi_api_key in the config; request a key at genomicintelligence.ai. The key is excluded from the cache key, so rotating it does not invalidate cached results.
No GPU is used. Inference runs on the vendor’s hardware, so these are CPU-local clients regardless of what is available on the host.
Every tool takes a list and returns one result per input, in order. That is the shape a Constraint or Optimizer consumes when scoring a population. A bare DNA string is accepted in place of a list.
Length bounds are checked locally before any request. Each task’s floor comes from its own published request schema; every task caps at 500,000 bp.
Leave model unset. The service resolves the current default per task, and pinning an identifier means a retired model fails hard. Enumerate the alternatives with GET /v1/tasks/{task}/models.
Errors carry a machine-readable code from a closed enum plus a request_id for support. Branch on the code rather than the HTTP status.
A malformed 2xx is refused, not coerced. A response that is well-formed HTTP but contradicts the published shape raises rather than parsing to zeros: a body that is not a {data, meta} envelope, or whose data is missing or empty, raises GIAPIError carrying the status and request_id; a field inside data that is documented as an object or an array and arrives as something else raises GIResponseShapeError naming that field. Absent and null members stay legitimate, since a task with nothing to report omits them.

Example notebook: See the full working example for a copy-paste-ready walkthrough.

Infrastructure Guides

The following guides cover how to run tools efficiently and at scale.

Tool Persistence

Keep a tool’s model warm across calls instead of reloading it every invocation.

Device Management

How GPUs are allocated to tools and how to target specific devices.

Parallel Execution

Fan a batch of inputs out across multiple GPUs.

​Background

​Learning Resources

​Tools

​GI Promoter (gi-promoter)

​API Reference

​Applications

​Usage Tips

​GI Splice Sites (gi-splice)

​API Reference

​Applications

​Usage Tips

​GI Enhancer Activity (gi-enhancer)

​API Reference

​Applications

​Usage Tips

​GI Chromatin State (gi-chromatin)

​API Reference

​Applications

​Usage Tips

​GI Gene Annotation (gi-annotation)

​API Reference

​Applications

​Usage Tips

​GI Gene Expression (gi-expression)

​API Reference

​Applications

​Usage Tips

​GI Find Genes and Predict Expression (gi-find-genes-and-predict-expression)

​API Reference

​Applications

​Usage Tips

​Toolkit Notes

​Infrastructure Guides

Tool Persistence

Device Management

Parallel Execution

Background

Learning Resources

Tools

GI Promoter (`gi-promoter`)

API Reference

Applications

Usage Tips

GI Splice Sites (`gi-splice`)

API Reference

Applications

Usage Tips

GI Enhancer Activity (`gi-enhancer`)

API Reference

Applications

Usage Tips

GI Chromatin State (`gi-chromatin`)

API Reference

Applications

Usage Tips

GI Gene Annotation (`gi-annotation`)

API Reference

Applications

Usage Tips

GI Gene Expression (`gi-expression`)

API Reference

Applications

Usage Tips

GI Find Genes and Predict Expression (`gi-find-genes-and-predict-expression`)

API Reference

Applications

Usage Tips

Toolkit Notes

Infrastructure Guides