drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/genomic-intelligence/references/sequence-acquisition.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
Sequence Acquisition (Ensembl)		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/757b63b1/skills/genomic-intelligence/references/sequence-acquisition.md	757b63b1	2026-07-24	prompt	accepted	upstream	false

Sequence Acquisition (Ensembl)

Turn a gene symbol or a genomic region into reference sequence so users don't have to bring a FASTA. Ensembl REST (rest.ensembl.org) is public — no key; only the prediction step needs a key (and only over REST).

On MCP, the acquisition tools (fetch_ensembl_sequence, fetch_region, fetch_gene_for_expression, find_genes) do this for you and return a handle. Over REST, query Ensembl yourself, then feed the sequence to /v1/tasks/....

Modes

• Full gene body (any task except expression) — resolve the gene, fetch its sequence.
• Coordinate range — fetch /sequence/region/{species}/{region}.
• Exact 9,198 bp TSS-centred window (expression only) — see below.

TSS-centring (why expression is special)

The expression model requires exactly 9,198 bp centred on the transcription start site (TSS). You cannot reliably build this from gene-body coordinates: the annotated gene start/end can sit far from the real TSS (HBB's gene end is 2,324 bp from its canonical TSS; ACTB's is 33,301 bp). Mis-centring tanks the prediction.

The correct construction: resolve the gene's canonical transcript (Ensembl expand=1), take the TSS from it (transcript start on the + strand, end on the − strand), and take 4,599 bp upstream + 4,598 bp downstream on the gene's strand = 9,198 bp; validate the length exactly. On MCP, fetch_gene_for_expression(gene=...) does all of this. Because it needs a transcript, it works from a gene, not a bare region.

Species & assembly

• Default: human, GRCh38.
• Non-human: use the Ensembl production name — lowercase, underscored: mus_musculus, drosophila_melanogaster, saccharomyces_cerevisiae. mouse / Drosophila will be rejected.
• The enhancer default (DeepSTARR) is Drosophila — match species to model (see tasks.md).

When to skip acquisition

Supply sequence directly when it is not reference genome — variant-bearing, edited, synthetic, or from a non-Ensembl assembly. Acquisition only returns reference sequence for the requested coordinates.

Limits

Bounded by the task's own cap (500,000 bp for most; exactly 9,198 bp for expression). Ensembl enforces its own per-request size limits; fetch very large ranges in pieces.