bio-blast

Original：🇺🇸 English

Translated

3 scriptsChecked / no sensitive code detected

NCBI BLAST sequence similarity search using BioPython. Use when a user wants to run BLAST programmatically with blastn/blastp and retrieve results in JSON format.

1installs

Sourcedakesan/cc-dnawork-plugin

Added on2026-02-14

NPX Install

npx skill4agent add dakesan/cc-dnawork-plugin bio-blast

SKILL.md Content

View Translation Comparison →

BLAST Search

NCBI BLAST (Basic Local Alignment Search Tool) を BioPython で実行し、結果を JSON 形式で取得するスキルです。

Quick Start

Install

bash

uv pip install biopython typer

Run with FASTA

bash

python scripts/run_blast_biopython.py --fasta path/to/query.fasta

Run with raw sequence

bash

python scripts/run_blast_biopython.py --sequence ATGCGATCG...

Restrict to organism (e.g., human)

bash

python scripts/run_blast_biopython.py --fasta query.fasta --organism "Homo sapiens"

Protein BLAST

bash

python scripts/run_blast_biopython.py --program blastp --database swissprot --sequence MTEYKLVVVG...

Save output

bash

python scripts/run_blast_biopython.py --fasta query.fasta --output blast_results.json

Output Format

Results are returned in JSON format with the following structure:

json

{
  "query": "No definition line",
  "query_length": 99,
  "database": "core_nt",
  "num_hits": 10,
  "hits": [
    {
      "rank": 1,
      "accession": "NM_007294",
      "title": "Homo sapiens BRCA1 DNA repair associated (BRCA1), mRNA",
      "e_value": 4.35e-43,
      "bit_score": 179.82,
      "percent_identity": 100.0,
      "identities": 99,
      "align_length": 99,
      "gaps": 0,
      "query_start": 1,
      "query_end": 99,
      "subject_start": 1,
      "subject_end": 99
    }
  ]
}

Command-line Options

```
--program
```
: BLAST program (blastn, blastp, blastx, tblastn, tblastx). Default: blastn
```
--database
```
: BLAST database (nt, nr, refseq_rna, swissprot, etc.). Default: nt
```
--fasta
```
: Path to FASTA file (single sequence only)
```
--sequence
```
: Raw query sequence string
```
--organism
```
: Restrict search to organism (e.g., "Homo sapiens")
```
--expect
```
: E-value threshold. Default: 0.001
```
--hitlist-size
```
: Maximum number of hits. Default: 10
```
--output
```
: Output path for JSON results

Best Practices

Save results - Don't re-run searches unnecessarily
Set E-value threshold - Default 10 is too permissive; use 0.001-0.01
Use gget for quick searches - Simpler API for single sequences
Cache parsed data - Avoid re-parsing large XML files
Handle rate limits - NCBI limits request frequency

BLAST vs BLAT

Aspect	BLAST	BLAT
Purpose	Similarity search	Genome mapping
Sensitivity	High	Medium
Speed	Medium	Very fast
Best for	Homolog search	Position finding

bio-blast

NPX Install

Tags

SKILL.md Content

BLAST Search

Quick Start

Install

Run with FASTA

Run with raw sequence

Restrict to organism (e.g., human)

Protein BLAST

Save output

Output Format

Command-line Options

Best Practices

BLAST vs BLAT