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blast-search

Execute NCBI BLAST searches via BioPython and output JSON results.

Updated Aug 23, 2026
Search Tags:#json#bioinformatics#biopython#NCBIWWW#NCBIXML#blast
One-click install
npx skills add https://github.com/dakesan/cc-dnawork-plugin --skill blast-search
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: blast-search
Source: https://github.com/dakesan/cc-dnawork-plugin/tree/main/scientific-skills/blast-search
Command: npx skills add https://github.com/dakesan/cc-dnawork-plugin --skill blast-search

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill enables programmatic BLAST searches (blastn, blastp, etc.) via BioPython and returns results in JSON, simplifying sequence similarity analysis workflows.

Core Features & Use Cases

  • BLAST Execution: Run BLAST (online or local) and fetch results.
  • Result Parsing: Convert BLAST results to JSON-ready structures.
  • Config Flexibility: Control program, database, organism filters, and output size.

Quick Start

Run a BLAST search against the nt database for a short query sequence and save results as JSON.

Frequently Asked Questions about blast-search

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

FAQPage Schema
How do I run BLAST searches programmatically and get results in JSON?▼

BLAST searches can be executed programmatically using BioPython's NCBIWWW.qblast for online searches or local BLAST installations. This Skill automates the workflow: submit your sequence (FASTA file or raw sequence), specify the program (blastn or blastp) and database, parse XML results with NCBIXML, and serialize output to JSON for downstream analysis.

Can I filter BLAST results by organism and control E-value thresholds?▼

Yes. This Skill supports optional organism filtering, E-value threshold configuration, and hitlist-size controls to refine result scope. These parameters are passed to the BLAST query, reducing noise and focusing hits on relevant sequences before JSON serialization.

What input formats does BLAST sequence search accept?▼

The Skill accepts both FASTA files and raw sequence strings as input. CLI validation enforces the --fasta or --sequence flag, ensuring your query is properly formatted before submission to NCBI BLAST or local databases.

How do I automate sequence similarity analysis across multiple sequences?▼

Provide sequences via FASTA files or command-line input, configure your BLAST program and database selection, and the Skill executes searches and returns structured JSON results. This enables batch processing and programmatic integration into bioinformatics pipelines.

What are the limitations when running BLAST searches online vs. locally?▼

Online BLAST via NCBIWWW has rate limits and network dependencies but requires no local database setup. Local BLAST requires downloaded databases but offers faster, unlimited queries. This Skill supports both; choose based on your throughput and infrastructure constraints.

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