tools-only Local BLAST - Usage Guide
Overview
This skill enables AI agents to help you run BLAST searches locally using BLAST+ command-line tools, enabling fast unlimited searches against custom or downloaded databases.
Prerequisites
Install BLAST+:
# macOS
brew install blast
# Ubuntu/Debian
sudo apt install ncbi-blast+
# conda
conda install -c bioconda blast
Verify:
blastn -version
Quick Start
Tell your AI agent what you want to do:
- "Create a BLAST database from my reference sequences"
- "BLAST my query against the local database"
- "Set up a local copy of the nt database"
- "Run reciprocal best BLAST between two species"
Example Prompts
Create Database
"Make a nucleotide BLAST database from references.fasta"
Run Search
"BLAST query.fasta against my_db with 8 threads"
Custom Output
"Run BLASTP and output tabular format with query ID, subject ID, percent identity, and E-value"
Large Scale
"I have 10,000 sequences to BLAST - set up an efficient workflow"
Best Hits
"Get only the best hit for each query sequence"
What the Agent Will Do
- Create BLAST databases with makeblastdb
- Run appropriate BLAST program (blastn, blastp, etc.)
- Configure output format (tabular, XML, etc.)
- Set performance options (threads, e-value)
- Parse and filter results as needed
When to Use Local vs Remote BLAST
Use Local When:
- Many queries to run
- Need fast turnaround
- Custom database
- Offline access needed
Use Remote When:
- One-off searches
- Need latest NCBI databases
- Don't want to install software
Tips
- Use -num_threads for faster searches
- -outfmt 6 gives easy-to-parse tabular output
- -max_target_seqs limits hits per query
- Create database with -parse_seqids to enable sequence extraction
- For large databases, consider downloading pre-built NCBI databases