bio-blat

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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.

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[Academic Research]

When & Why to Use This Skill

This Claude skill enables researchers to perform local BLAT (Blast-like Alignment Tool) searches for DNA sequence alignment against human genome references like hg38 and CHM13. By utilizing local .2bit reference files, it provides a high-performance, private, and reliable alternative to external UCSC API dependencies, streamlining genomic data analysis workflows.

Use Cases

  • Genomic Mapping: Aligning specific DNA sequences or FASTA files to the hg38 or CHM13 reference genomes to identify precise chromosomal coordinates and structural variants.
  • Offline Bioinformatics Research: Conducting sequence alignments in secure or restricted network environments where external API access is unavailable or prohibited due to data privacy concerns.
  • High-Throughput Sequence Processing: Executing large-scale DNA alignments locally to bypass the rate limits, latency, and connectivity issues associated with public genomic web services.
namebio-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_invocabletrue

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)

  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.