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blat-api-searching

Runs local BLAT searches for DNA sequences using hg38 or CHM13 references.

Updated Aug 27, 2026
Search Tags:#genomics#local-alignment#blat#2bit#psl
One-click install
npx skills add https://github.com/dakesan/cc-dnawork-plugin --skill blat-api-searching
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: blat-api-searching
Source: https://github.com/dakesan/cc-dnawork-plugin/tree/main/scientific-skills/blat-api-searching
Command: npx skills add https://github.com/dakesan/cc-dnawork-plugin --skill blat-api-searching

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires typer, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill enables local BLAT searches against hg38 or CHM13 using downloaded 2bit references, providing PSL outputs and JSON-ready results without relying on external web services.

Core Features & Use Cases

  • Local BLAT: Run BLAT searches with local 2bit references.
  • PSL Parsing: Parse PSL/PSL-like outputs into structured data.
  • Reference Management: Automatically download and manage 2bit references for hg38 and CHM13.

Quick Start

Run a local BLAT search against hg38 with a query FASTA and output results to blat.json.

Frequently Asked Questions about blat-api-searching

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I run BLAT searches locally without internet access?▼

Local BLAT searches use downloaded 2bit reference files stored in ~/.local/share/blat, enabling offline DNA sequence alignment against hg38 or CHM13 without relying on web services. This approach works in restricted-network environments where external BLAT servers are unavailable.

What's the difference between PSL output and JSON format for BLAT results?▼

PSL is the standard BLAT alignment output format containing tab-separated columns. This Skill parses PSL results into JSON-structured data, making alignments machine-readable and easier to integrate into downstream analysis pipelines.

Can I use BLAT with FASTA files or raw DNA sequences?▼

The Skill accepts both single-sequence FASTA files and raw DNA sequences as input. Query sequences are processed through BLAT and output as PSL-derived JSON results compatible with further analysis.

What do I need to set up before running local BLAT searches?▼

You need Python, the typer CLI framework, the blat and curl tools installed, and a 2bit reference file (hg38 or CHM13) downloaded and stored under ~/.local/share/blat. The Skill can automate reference download and management.

When should I use local BLAT instead of web-based alignment services?▼

Local BLAT is essential in offline environments, restricted networks, or when processing sensitive genomic data that cannot be uploaded to external servers. It provides the same alignment accuracy with full control over your reference data and results.

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