---

name: bio-blat description: "Runs local BLAT searches for DNA sequence alignment against hg38 or CHM13 using local .2bit references. Use when a user wants to align a DNA sequence without relying on UCSC API access." user_invocable: true

BLAT API Searching

Quick start

Run BLAT locally via the Python CLI script. The script manages reference downloads.

Utility script

Install dependencies:

Copyuv pip install typer

Run BLAT with a FASTA file:

Copypython scripts/run_blat_local.py run --reference hg38 --fasta path/to/query.fasta

Run BLAT with a raw sequence:

Copypython scripts/run_blat_local.py run --reference CHM13 --sequence ACTG...

Save JSON output to a file:

Copypython scripts/run_blat_local.py run --reference hg38 --sequence ACTG... --output blat.json

When to read references

• Local BLAT setup and references: See references/local_blat.md

Workflow (local-only)

1. Confirm the reference assembly (hg38 or CHM13).
2. Ensure the 2bit reference exists in ~/.local/share/blat.
3. Use the CLI script to run BLAT and get a PSL output.
4. If FASTA has multiple sequences, split into one sequence per file.