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

uv pip install biopython typer

Run with FASTA

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

Run with raw sequence

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

Restrict to organism (e.g., human)

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

Protein BLAST

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

Save output

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:

{
  "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

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

BLAST vs BLAT