biopython

Name: biopython
Author: LeonChaoX

41installs61forks

How to install biopython?

leonchaox/qinyan-academic-skills/biopython

$npx -y skills add LeonChaoX/qinyan-academic-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

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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 1.85 (released January 2025), which supports Python 3 and requires NumPy.
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 Biopython using pip (requires Python 3 and NumPy):
39
40	```python
41	uv pip install biopython
42	```
43
44	For NCBI database access, always set your email address (required by NCBI):
45
46	```python
47	from Bio import Entrez
48	Entrez.email = "your.email@example.com"
49
50	# Optional: API key for higher rate limits (10 req/s instead of 3 req/s)
51	Entrez.api_key = "your_api_key_here"
52	```
53
54	## Using This Skill
55
56	This skill provides comprehensive documentation organized by functionality area. When working on a task, consult the relevant reference documentation:
57
58	### 1. Sequence Handling (Bio.Seq & Bio.SeqIO)
59
60	Reference: `references/sequence_io.md`
61
62	Use for:
63	- Creating and manipulating biological sequences
64	- Reading and writing sequence files (FASTA, GenBank, FASTQ, etc.)
65	- Converting between file formats
66	- Extracting sequences from large files
67	- Sequence translation, transcription, and reverse complement
68	- Working with SeqRecord objects
69
70	Quick example:
71	```python
72	from Bio import SeqIO
73
74	# Read sequences from FASTA file
75	for record in SeqIO.parse("sequences.fasta", "fasta"):
76	print(f"{record.id}: {len(record.seq)} bp")
77
78	# Convert GenBank to FASTA
79	SeqIO.convert("input.gb", "genbank", "output.fasta", "fasta")
80	```
81
82	### 2. Alignment Analysis (Bio.Align & Bio.AlignIO)
83
84	Reference: `references/alignment.md`
85
86	Use for:
87	- Pairwise sequence alignment (global and local)
88	- Reading and writing multiple sequence alignments
89	- Using substitution matrices (BLOSUM, PAM)
90	- Calculating alignment statistics
91	- Customizing alignment parameters
92
93	Quick example:
94	```python
95	from Bio import Align
96
97	# Pairwise alignment
98	aligner = Align.PairwiseAligner()
99	aligner.mode = 'global'
100	alignments = aligner.align("ACCGGT", "ACGGT")
101	print(alignments[0])
102	```
103
104	### 3. Database Access (Bio.Entrez)
105
106	Reference: `references/databases.md`
107
108	Use for:
109	- Searching NCBI databases (PubMed, GenBank, Protein, Gene, etc.)
110	- Downloading sequences and records
111	- Fetching publication information
112	- Finding related records across databases
113	- Batch downloading with proper rate limiting
114
115	Quick example:
116	```python
117	from Bio import Entrez
118	Entrez.email = "your.email@example.com"
119
120	# Search PubMed
121	handle = Entrez.esearch(db="pubmed", term="biopython", retmax=10)
122	results = Entrez.read(handle)
123	handle.close()
124	print(f"Found {results['Count']} results")
125	```
126
127	### 4. BLAST Operations (Bio.Blast)
128
129	Reference: `references/blast.md`
130
131	Use for:
132	- Running BLAST searches via NCBI web services
133	- Running local BLAST searches
134	- Parsing BLAST XML output
135	- Filtering results by E-value or identity
136	- Extracting hit sequences
137
138	Quick example:
139	```python
140	f

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biopython

41installs61forks

View on GitHub

How to install biopython?

leonchaox/qinyan-academic-skills/biopython

$npx -y skills add LeonChaoX/qinyan-academic-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 1.85 (released January 2025), which supports Python 3 and requires NumPy.
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 Biopython using pip (requires Python 3 and NumPy):
39
40	```python
41	uv pip install biopython
42	```
43
44	For NCBI database access, always set your email address (required by NCBI):
45
46	```python
47	from Bio import Entrez
48	Entrez.email = "your.email@example.com"
49
50	# Optional: API key for higher rate limits (10 req/s instead of 3 req/s)
51	Entrez.api_key = "your_api_key_here"
52	```
53
54	## Using This Skill
55
56	This skill provides comprehensive documentation organized by functionality area. When working on a task, consult the relevant reference documentation:
57
58	### 1. Sequence Handling (Bio.Seq & Bio.SeqIO)
59
60	Reference: `references/sequence_io.md`
61
62	Use for:
63	- Creating and manipulating biological sequences
64	- Reading and writing sequence files (FASTA, GenBank, FASTQ, etc.)
65	- Converting between file formats
66	- Extracting sequences from large files
67	- Sequence translation, transcription, and reverse complement
68	- Working with SeqRecord objects
69
70	Quick example:
71	```python
72	from Bio import SeqIO
73
74	# Read sequences from FASTA file
75	for record in SeqIO.parse("sequences.fasta", "fasta"):
76	print(f"{record.id}: {len(record.seq)} bp")
77
78	# Convert GenBank to FASTA
79	SeqIO.convert("input.gb", "genbank", "output.fasta", "fasta")
80	```
81
82	### 2. Alignment Analysis (Bio.Align & Bio.AlignIO)
83
84	Reference: `references/alignment.md`
85
86	Use for:
87	- Pairwise sequence alignment (global and local)
88	- Reading and writing multiple sequence alignments
89	- Using substitution matrices (BLOSUM, PAM)
90	- Calculating alignment statistics
91	- Customizing alignment parameters
92
93	Quick example:
94	```python
95	from Bio import Align
96
97	# Pairwise alignment
98	aligner = Align.PairwiseAligner()
99	aligner.mode = 'global'
100	alignments = aligner.align("ACCGGT", "ACGGT")
101	print(alignments[0])
102	```
103
104	### 3. Database Access (Bio.Entrez)
105
106	Reference: `references/databases.md`
107
108	Use for:
109	- Searching NCBI databases (PubMed, GenBank, Protein, Gene, etc.)
110	- Downloading sequences and records
111	- Fetching publication information
112	- Finding related records across databases
113	- Batch downloading with proper rate limiting
114
115	Quick example:
116	```python
117	from Bio import Entrez
118	Entrez.email = "your.email@example.com"
119
120	# Search PubMed
121	handle = Entrez.esearch(db="pubmed", term="biopython", retmax=10)
122	results = Entrez.read(handle)
123	handle.close()
124	print(f"Found {results['Count']} results")
125	```
126
127	### 4. BLAST Operations (Bio.Blast)
128
129	Reference: `references/blast.md`
130
131	Use for:
132	- Running BLAST searches via NCBI web services
133	- Running local BLAST searches
134	- Parsing BLAST XML output
135	- Filtering results by E-value or identity
136	- Extracting hit sequences
137
138	Quick example:
139	```python
140	f

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Type