Why use local BLAT instead of the UCSC web interface?

Local BLAT offers better data privacy for sensitive sequences, avoids internet latency, and bypasses the rate limits associated with public APIs.

Can I process multiple sequences at once?

Yes, you can provide a FASTA file containing multiple sequences, and the utility script handles the alignment for each sequence.

What output formats does the skill provide?

The tool can generate standard PSL output or structured JSON files for easy integration into other data pipelines.

Which human genome references are supported?

The skill currently supports the hg38 (GRCh38) and CHM13 (T2T) reference assemblies.

Do I need an internet connection for every search?

No, once the .2bit reference files are downloaded to your local machine, all sequence alignments are performed entirely offline.

Local BLAT DNA Alignment

Name: Local BLAT DNA Alignment
Author: dakesan

bydakesan

Data Science & ML

Performs high-speed local DNA sequence alignment against hg38 and CHM13 genomic references without external API dependencies.

About

The BLAT API Searching skill enables Claude to perform local genomic sequence alignments using the Blast-like Alignment Tool (BLAT). It simplifies bioinformatics workflows by automating the management of reference downloads (hg38/CHM13), handling FASTA files, and executing searches directly against local .2bit files. This tool is ideal for researchers requiring data privacy, offline capabilities, or high-throughput processing that bypasses the rate limits of public UCSC API endpoints.

Key Features

Automatic management and downloading of .2bit reference files
Flexible input handling via FASTA files or raw DNA sequences
0 GitHub stars
Support for hg38 and CHM13 genomic reference assemblies
Local BLAT search execution without external API calls
Structured output generation in JSON or PSL formats

Use Cases

Comparing sequence variations between hg38 and CHM13 assemblies
Identifying genomic coordinates for private DNA sequences
Aligning large batches of FASTA sequences against human references

About

Key Features

Automatic management and downloading of .2bit reference files
Flexible input handling via FASTA files or raw DNA sequences
0 GitHub stars
Support for hg38 and CHM13 genomic reference assemblies
Local BLAT search execution without external API calls
Structured output generation in JSON or PSL formats

Use Cases

Comparing sequence variations between hg38 and CHM13 assemblies
Identifying genomic coordinates for private DNA sequences
Aligning large batches of FASTA sequences against human references