Genomic Intelligence

Genomic Intelligence — DNA Sequence Models

Genomic Intelligence (GI) serves transformer DNA language models over six

sequence-analysis tasks on managed GPUs. Give it a gene symbol, a **genomic

region, or a DNA/FASTA sequence**; it returns structured predictions —

promoter regions, splice sites, enhancer activity, chromatin state, expression

(log TPM), and de-novo gene annotation. Nothing runs locally: no model weights,

no GPU, no heavy Python stack. It is a thin client over a hosted, versioned

inference API.

Official docs: docs.genomicintelligence.ai ·

REST contract at api.genomicintelligence.ai/v1/openapi.json ·

hosted MCP server at https://mcp.genomicintelligence.ai/mcp

When to use this skill

Use GI when the user has DNA and wants a model prediction:

• Find promoters in a genomic region (promoter)
• Predict splice donor/acceptor sites (splice)
• Score enhancer activity — developmental & housekeeping (enhancer)
• Annotate chromatin state across hundreds of tracks (chromatin)
• Predict expression as log(TPM+1) from a sequence + cell-type context (expression)
• Annotate genes/transcripts de novo, no reference needed (annotation)
• Find the genes in a region and predict each one's expression (composite)

Not for local alignment, variant calling, or file I/O — use a local tool

(BioPython, bcftools) for those. GI is for model inference from sequence.

> For research and development use, not clinical or diagnostic decisions.

Two ways to call GI

Hosted MCP server (best for AI agents — keyless)

GI hosts an MCP server at https://mcp.genomicintelligence.ai/mcp (Streamable

HTTP). When your agent host supports MCP, prefer it: it works keyless against

a capped public demo quota (zero setup), and an optional gi_ bearer key raises

the quota. It exposes acquisition tools that return a sequence handle

(sequence_ref) and predict_* tools that take that handle — so large sequences

never bloat the context. See MCP workflow below and

references/mcp.md.

REST API (universal)

Plain HTTP with requests against https://api.genomicintelligence.ai/v1. The

REST path requires a GI_API_KEY (a gi_ bearer). Use it on any host, in

scripts, or when you need the raw envelope. See Core REST workflow.

Access and authentication

• The hosted MCP demo is keyless — try it with nothing set.
• The REST /v1 API needs a key, sent as Authorization: Bearer <key>.

Request one at [email protected].

• Never hardcode the key. Read it from the GI_API_KEY environment variable

(or a .env via python-dotenv). Never commit keys.

export GI_API_KEY="gi_yourkeyhere"     # optional for MCP; required for REST
export GI_BASE_URL="https://api.genomicintelligence.ai"   # override for staging

Keys are scoped to a partner tier with concurrency and per-minute caps. A 429

means you hit a cap — back off and retry, or ask GI to raise your tier.

The six tasks

All REST tasks share one shape: POST /v1/tasks/{task}/predict with body

{sequence, sequence_name, model?, options?}, returning a {data, meta}

envelope. What differs per task:

| Task | Mode | Length bound | Notes |

|---|---|---|---|

| promoter | sync | 1–500,000 bp | sliding-window promoter regions |

| splice | sync | 1–500,000 bp | donor/acceptor sites (long-context BigBird) |

| enhancer | sync | 1–500,000 bp | dev + housekeeping scores (DeepSTARR, *Drosophila*) |

| chromatin | sync | 1–500,000 bp | hundreds of tracks (DeepSEA) |

| expression | sync | exactly 9,198 bp | log(TPM+1); needs a cell-type description |

| annotation | async | 1–500,000 bp | de-novo transcripts; submit + poll |

Omit model and the API uses the task's default — that is the recommended

call. Default model IDs are intentionally not documented here: defaults

change and retired IDs fail hard, so never hardcode one. To pin a model, or to

pick a non-human one (Drosophila, yeast, and Arabidopsis models exist for several

tasks), discover IDs at call time with GET /v1/tasks/{task}/models (REST) or

list_models (MCP) — and never invent one. Full per-task output shapes are

in references/tasks.md.

Two hard rules the model enforces:

• expression needs exactly 9,198 bp, a window centred on the TSS

(4,599 upstream + TSS + 4,598 downstream). Any other length is rejected. Use the acquisition helpers below to

build it — do not truncate by hand.

• expression needs a description — a cell-type / assay string (e.g.

"K562 cells"), passed as options.description.

Sequence acquisition

You rarely start from a raw 9,198 bp string. Acquire sequence first:

• From a gene symbol → MCP fetch_ensembl_sequence(gene=...); **from

coordinates** → fetch_region(region=...). Both fetch public Ensembl reference

sequence (no key). REST users can query Ensembl REST directly. (find_genes is

the annotation task, not an acquisition tool.)

• For expression → use the TSS-centred fetch so the window is exactly

9,198 bp. MCP: fetch_gene_for_expression (handles the centring). Do not

build the window by hand.

• From a local FASTA → MCP store_inline_sequence, or read the file yourself

for REST. (load_local_fasta exists only in local deployments, not on the

hosted server.)

• A demo sequence → MCP load_demo_sequence(name=...) returns a ready handle

(great for a keyless smoke test); name is required.

See references/sequence-acquisition.md for the exact Ensembl calls and the

expression-window math.

Core REST workflow

Sync tasks (promoter, splice, enhancer, chromatin, expression) are one call:

import os, requests

BASE = os.environ.get("GI_BASE_URL", "https://api.genomicintelligence.ai")
HEADERS = {"Authorization": f"Bearer {os.environ['GI_API_KEY']}"}

def predict(task, sequence, sequence_name, model=None, options=None):
    body = {"sequence": sequence, "sequence_name": sequence_name}
    if model:   body["model"] = model
    if options: body["options"] = options
    r = requests.post(f"{BASE}/v1/tasks/{task}/predict", headers=HEADERS, json=body)
    r.raise_for_status()          # 400 invalid; 401 no/bad key; 413 too long; 429 rate limit
    return r.json()               # {"data": {...}, "meta": {...}}

# Promoter:
out = predict("promoter", seq, "TP53_region")
print(out["data"]["summary"])

# Expression — exactly 9,198 bp + a cell-type description:
out = predict("expression", tss_window_9198bp, "HBB",
              options={"description": "K562 cells"})
print(out["data"]["prediction"]["expression_log_tpm"])

Async: annotation

annotation is submit-then-poll. Send Prefer: respond-async, get a job_id,

poll until terminal:

import time

r = requests.post(f"{BASE}/v1/tasks/annotation/predict",
                  headers={**HEADERS, "Prefer": "respond-async"},
                  json={"sequence": seq, "sequence_name": "TP53"})
r.raise_for_status()              # 202 Accepted
job_id = r.json()["data"]["job_id"]

while True:
    j = requests.get(f"{BASE}/v1/tasks/jobs/{job_id}", headers=HEADERS)
    if j.status_code == 200:      # terminal: body is the final {data, meta}
        break
    j.raise_for_status()          # 202 = still running (2xx, won't raise)
    time.sleep(5)                 # ~20 s typical for ~20 kb
transcripts = j.json()["data"]["transcripts"]

MCP workflow (handle-based)

On an MCP host, acquire a handle, then predict against it — sequences stay out of

the context:

# 1. Acquire a sequence handle (each returns a sequence_ref):
load_demo_sequence(name="promoter_tp53")  # keyless smoke test; `name` is REQUIRED
fetch_ensembl_sequence(gene="TP53")       # gene symbol or Ensembl ID -> handle
fetch_region(region="chr11:5,225,000-5,235,000")   # coordinates -> handle
fetch_gene_for_expression(gene="HBB")     # TSS-centred 9,198 bp handle for expression

# 2. Predict against the handle:
predict_promoter(sequence_ref=<ref>)
predict_expression(sequence_ref=<ref>, description="K562 cells")
predict_splice(sequence_ref=<ref>)        # + predict_enhancer / predict_chromatin

# 3. Annotation on MCP is `find_genes` (there is no predict_annotation).
#    It takes a handle, not a region, and runs async internally:
find_genes(sequence_ref=<ref>)            # wait=True (default) returns the result
find_genes(sequence_ref=<ref>, wait=False)  # -> job_id; poll get_job(job_id)

# Discover models with list_models(task); reference context lives in the
# gi://models, gi://docs/tasks, and gi://account MCP resources.

Composite: find genes, then predict expression

To answer "what genes are in this region and how are they expressed?", use the

composite:

• MCP: find_genes_and_predict_expression(sequence_ref=..., description=...)

— takes a handle, not a region (acquire one with fetch_region first);

description is required. Finds genes in the sequence and returns an

expression prediction for each.

• REST: call gene discovery, then loop expression per gene (build each

TSS-centred 9,198 bp window via the acquisition helpers).

Errors

| Code | Meaning | Action |

|---|---|---|

| 400 | Invalid request / bad sequence | Check the body; expression must be exactly 9,198 bp and carry description |

| 401 | Missing/invalid key (REST) | Set GI_API_KEY; or use the keyless MCP demo |

| 413 | Sequence too long | Stay within the task's length bound (≤500,000 bp) |

| 429 | Rate / concurrency cap | Back off and retry; ask GI to raise your tier |

| 422 | Validation failed (validation_failed) | The most common failure: expression not exactly 9,198 bp, or a sequence below the model's minimum length |

| 5xx | Server error | Retry; if persistent, contact support |

Reference files

• references/tasks.md — per-task output shapes, model registries, the async

annotation contract.

• references/api-and-auth.md — REST endpoints, the {data, meta} envelope,

auth, base-URL override, tiers.

• references/mcp.md — the hosted MCP tool list, the handle-based flow, and the

gi:// resources.

• references/sequence-acquisition.md — Ensembl fetch calls and the

expression-window (9,198 bp, TSS-centred) math.