biopython

Name: biopython
Author: K-Dense-AI

842installs3.1kforks

How to install biopython?

k-dense-ai/scientific-agent-skills/biopython

$npx -y skills add K-Dense-AI/scientific-agent-skills --skill biopython

Installs into the current project.

Summary

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for

Files · 1

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SKILL.md

1	# Biopython: Computational Molecular Biology in Python
2
3	## Overview
4
5	Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks. The current version is Biopython 1.87 (released 30 March 2026). It supports Python 3.10-3.14 and PyPy3.10, and requires NumPy. Biopython 1.87 also addresses CVE-2025-68463 in `Bio.Entrez.Parser` when parsing untrusted files, so prefer 1.87+ for workflows that parse externally supplied Entrez XML.
6
7	## When to Use This Skill
8
9	Use this skill when:
10
11	- Working with biological sequences (DNA, RNA, or protein)
12	- Reading, writing, or converting biological file formats (FASTA, GenBank, FASTQ, PDB, mmCIF, etc.)
13	- Accessing NCBI databases (GenBank, PubMed, Protein, Gene, etc.) via Entrez
14	- Running BLAST searches or parsing BLAST results
15	- Performing sequence alignments (pairwise or multiple sequence alignments)
16	- Analyzing protein structures from PDB files
17	- Creating, manipulating, or visualizing phylogenetic trees
18	- Finding sequence motifs or analyzing motif patterns
19	- Calculating sequence statistics (GC content, molecular weight, melting temperature, etc.)
20	- Performing structural bioinformatics tasks
21	- Working with population genetics data
22	- Any other computational molecular biology task
23
24	## Core Capabilities
25
26	Biopython is organized into modular sub-packages, each addressing specific bioinformatics domains:
27
28	1. Sequence Handling - Bio.Seq and Bio.SeqIO for sequence manipulation and file I/O
29	2. Alignment Analysis - Bio.Align and Bio.AlignIO for pairwise and multiple sequence alignments
30	3. Database Access - Bio.Entrez for programmatic access to NCBI databases
31	4. BLAST Operations - Bio.Blast for running and parsing BLAST searches
32	5. Structural Bioinformatics - Bio.PDB for working with 3D protein structures
33	6. Phylogenetics - Bio.Phylo for phylogenetic tree manipulation and visualization
34	7. Advanced Features - Motifs, population genetics, sequence utilities, and more
35
36	## Installation and Setup
37
38	Install the current stable Biopython release with an explicit version pin for reproducibility:
39
40	```bash
41	uv pip install "biopython==1.87"
42	```
43
44	For NCBI database access, always set your email address (required by NCBI). For reusable software, set a stable `Entrez.tool` value and register the tool/email with NCBI. For higher rate limits (10 req/s instead of 3 req/s), read only `NCBI_API_KEY` from the environment — do not hardcode keys or load unrelated environment variables:
45
46	```python
47	import os
48	from Bio import Entrez
49
50	Entrez.email = "your.email@example.com" # required — use your real email
51	Entrez.tool = "your_tool_name" # optional but recommended for reusable software
52
53	# Optional: register at https://www.ncbi.nlm.nih.gov/account/settings/
54	if api_key := os.environ.get("NCBI_API_KEY"):
55	Entrez.api_key = api_key
56	```
57
58	## Using This Skill
59
60	This skill provides comprehensive documentation organized by functionality area. When working on a task, consult the relevant reference documentation:
61
62	### 1. Sequence Handling (Bio.Seq & Bio.SeqIO)
63
64	Reference: `references/sequence_io.md`
65
66	Use for:
67	- Creating and manipulating biological sequences
68	- Reading and writing sequence files (FASTA, GenBank, FASTQ, etc.)
69	- Converting between file formats
70	- Extracting sequences from large files
71	- Sequence translation, transcription, and reverse complement
72	- Working with SeqRecord objects
73
74	Quick example:
75	```python
76	from Bio import SeqIO
77
78	# Read sequences from FASTA file
79	for record in SeqIO.parse("sequences.fasta", "fasta"):
80	print(f"{record.id}

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biopython

842installs3.1kforks

View on GitHub

How to install biopython?

k-dense-ai/scientific-agent-skills/biopython

$npx -y skills add K-Dense-AI/scientific-agent-skills --skill biopython

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# Biopython: Computational Molecular Biology in Python
2
3	## Overview
4
5	Biopython is a comprehensive set of freely available Python tools for biological computation. It provides functionality for sequence manipulation, file I/O, database access, structural bioinformatics, phylogenetics, and many other bioinformatics tasks. The current version is Biopython 1.87 (released 30 March 2026). It supports Python 3.10-3.14 and PyPy3.10, and requires NumPy. Biopython 1.87 also addresses CVE-2025-68463 in `Bio.Entrez.Parser` when parsing untrusted files, so prefer 1.87+ for workflows that parse externally supplied Entrez XML.
6
7	## When to Use This Skill
8
9	Use this skill when:
10
11	- Working with biological sequences (DNA, RNA, or protein)
12	- Reading, writing, or converting biological file formats (FASTA, GenBank, FASTQ, PDB, mmCIF, etc.)
13	- Accessing NCBI databases (GenBank, PubMed, Protein, Gene, etc.) via Entrez
14	- Running BLAST searches or parsing BLAST results
15	- Performing sequence alignments (pairwise or multiple sequence alignments)
16	- Analyzing protein structures from PDB files
17	- Creating, manipulating, or visualizing phylogenetic trees
18	- Finding sequence motifs or analyzing motif patterns
19	- Calculating sequence statistics (GC content, molecular weight, melting temperature, etc.)
20	- Performing structural bioinformatics tasks
21	- Working with population genetics data
22	- Any other computational molecular biology task
23
24	## Core Capabilities
25
26	Biopython is organized into modular sub-packages, each addressing specific bioinformatics domains:
27
28	1. Sequence Handling - Bio.Seq and Bio.SeqIO for sequence manipulation and file I/O
29	2. Alignment Analysis - Bio.Align and Bio.AlignIO for pairwise and multiple sequence alignments
30	3. Database Access - Bio.Entrez for programmatic access to NCBI databases
31	4. BLAST Operations - Bio.Blast for running and parsing BLAST searches
32	5. Structural Bioinformatics - Bio.PDB for working with 3D protein structures
33	6. Phylogenetics - Bio.Phylo for phylogenetic tree manipulation and visualization
34	7. Advanced Features - Motifs, population genetics, sequence utilities, and more
35
36	## Installation and Setup
37
38	Install the current stable Biopython release with an explicit version pin for reproducibility:
39
40	```bash
41	uv pip install "biopython==1.87"
42	```
43
44	For NCBI database access, always set your email address (required by NCBI). For reusable software, set a stable `Entrez.tool` value and register the tool/email with NCBI. For higher rate limits (10 req/s instead of 3 req/s), read only `NCBI_API_KEY` from the environment — do not hardcode keys or load unrelated environment variables:
45
46	```python
47	import os
48	from Bio import Entrez
49
50	Entrez.email = "your.email@example.com" # required — use your real email
51	Entrez.tool = "your_tool_name" # optional but recommended for reusable software
52
53	# Optional: register at https://www.ncbi.nlm.nih.gov/account/settings/
54	if api_key := os.environ.get("NCBI_API_KEY"):
55	Entrez.api_key = api_key
56	```
57
58	## Using This Skill
59
60	This skill provides comprehensive documentation organized by functionality area. When working on a task, consult the relevant reference documentation:
61
62	### 1. Sequence Handling (Bio.Seq & Bio.SeqIO)
63
64	Reference: `references/sequence_io.md`
65
66	Use for:
67	- Creating and manipulating biological sequences
68	- Reading and writing sequence files (FASTA, GenBank, FASTQ, etc.)
69	- Converting between file formats
70	- Extracting sequences from large files
71	- Sequence translation, transcription, and reverse complement
72	- Working with SeqRecord objects
73
74	Quick example:
75	```python
76	from Bio import SeqIO
77
78	# Read sequences from FASTA file
79	for record in SeqIO.parse("sequences.fasta", "fasta"):
80	print(f"{record.id}

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Type