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BLAT API Searching
bio-blat
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.
SKILL.md
Full skill instructions
BLAT API Searching
Quick start
Run BLAT locally via the Python CLI script. The script manages reference downloads.
Utility script
Install dependencies:
uv pip install typer
Run BLAT with a FASTA file:
python scripts/run_blat_local.py run --reference hg38 --fasta path/to/query.fasta
Run BLAT with a raw sequence:
python scripts/run_blat_local.py run --reference CHM13 --sequence ACTG...
Save JSON output to a file:
python 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)
- Confirm the reference assembly (
hg38orCHM13). - Ensure the 2bit reference exists in
~/.local/share/blat. - Use the CLI script to run BLAT and get a PSL output.
- If FASTA has multiple sequences, split into one sequence per file.
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