biopython-bio
"Bioinformatics operations via Biopython. Use when: user asks about DNA/protein sequences, BLAST, or PDB structures. NOT for: clinical genomics or variant calling pipelines."
소스 정보
- 저장소
- beita6969/ScienceClaw
- 최근 소스 활동
- 2026년 3월 12일 04:53
- 감지된 SKILL.md 언어
- 영어
- 스타
- 904
- 포크
- 104
설치 방법
기본적으로 소스를 먼저 확인하는 Prompt가 선택됩니다. 직접 명령으로 전환하거나 로컬 사본을 다운로드할 수도 있습니다.
소스 파일 검토
설치 여부를 결정하기 전에 SKILL.md와 SkillsMP에 표시된 보조 파일을 읽어 보세요.
SKILL.md 표시 중
SKILL.md
소스 지침 · 읽기 전용 미리보기- name
- biopython-bio
- description
- Bioinformatics operations via Biopython. Use when: user asks about DNA/protein sequences, BLAST, or PDB structures. NOT for: clinical genomics or variant calling pipelines.
- metadata
- {"openclaw":{"emoji":"🧬","requires":{"bins":"[Truncated]"},"install":["[Truncated]"]}}
# Biopython Bio
Bioinformatics operations using Biopython.
## When to Use
- Reading/writing sequence files (FASTA, GenBank)
- Running BLAST searches (local or remote NCBI)
- Sequence alignment and manipulation
- Parsing PDB protein structures
- Phylogenetic tree construction
- Querying NCBI Entrez databases
## When NOT to Use
- Clinical genomics or variant calling (use GATK, bcftools)
- RNA-seq differential expression (use DESeq2, edgeR)
- Genome assembly (use SPAdes, Canu)
- Molecular dynamics simulations (use GROMACS, OpenMM)
## Sequence Reading and Writing
```python
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
for record in SeqIO.parse('sequences.fasta', 'fasta'):
print(f"{record.id}: {len(record.seq)} bp")
# Write FASTA
records = [SeqRecord(Seq('ATGCGATCGATCG'), id='seq1', description='example')]
SeqIO.write(records, 'output.fasta', 'fasta')
```
## Sequence Manipulation
```python
from Bio.Seq import Seq
from Bio.SeqUtils import gc_fraction, molecular_weight
dna = Seq('ATGCGATCGATCGATCG')
rev_comp = dna.reverse_complement()
protein = dna.translate()
gc = gc_fraction(dna)
mw = molecular_weight(dna, seq_type='DNA')
```
## BLAST Searches
```python
from Bio.Blast import NCBIWWW, NCBIXML
result_handle = NCBIWWW.qblast('blastn', 'nt', 'ATGCGATCGATCGATCG')
for record in NCBIXML.parse(result_handle):
for aln in record.alignments:
for hsp in aln.hsps:
if hsp.expect < 1e-10:
print(f"{aln.title[:60]}, E={hsp.expect}")
```
## Pairwise Alignment
```python
from Bio import Align
aligner = Align.PairwiseAligner()
aligner.mode = 'global'
aligner.match_score = 2
aligner.mismatch_score = -1
best = aligner.align('ATCGATCGATCG', 'ATCAATCAATCG')[0]
print(best, f"Score: {best.score}")
```
## PDB Structure Parsing
```python
from Bio.PDB import PDBParser, PDBList
structure = PDBParser(QUIET=True).get_structure('prot', 'structure.pdb')
for chain in structure[0]:
for res in chain:
if res.id[0] == ' ' and 'CA' in res:
print(f"{res.resname} {res.id[1]}: {res['CA'].coord}")
```
## Entrez Queries and Phylogenetics
```python
from Bio import Entrez, Phylo, AlignIO
from Bio.Phylo.TreeConstruction import DistanceCalculator, DistanceTreeConstructor
Entrez.email = 'your.email@example.com' # Required by NCBI
handle = Entrez.esearch(db='pubmed', term='CRISPR AND 2025[pdat]', retmax=5)
record = Entrez.read(handle)
# Phylogenetics from alignment
aln = AlignIO.read('aligned.fasta', 'fasta')
tree = DistanceTreeConstructor().nj(DistanceCalculator('identity').get_distance(aln))
Phylo.draw_ascii(tree)
```
## Quick One-liner
```bash
python3 -c "
from Bio.Seq import Seq
dna = Seq('ATGAAAGCTTGA')
print(f'Protein: {dna.translate()}, RevComp: {dna.reverse_complement()}')
"
```
## Best Practices
1. Always set `Entrez.email` before NCBI queries.
2. Respect NCBI rate limits: max 3 requests/second without API key.
3. Use `QUIET=True` in PDB parser to suppress warnings.
4. Check sequence type before operations like `translate()`.
5. For large BLAST jobs, prefer local BLAST+ over remote NCBI.
GitHub에서 보기