# Examples
Common workflows and use cases for BioPython MCP.
## Basic Sequence Analysis
### Analyze a DNA Sequence
```
1. Calculate GC content
Tool: calculate_gc_content
Input: {"sequence": "ATGGCCATTGTAATGGGCCGC"}
2. Find start codons
Tool: find_motif
Input: {"sequence": "ATGGCCATTGTAATGGGCCGC", "motif": "ATG"}
3. Translate to protein
Tool: translate_sequence
Input: {"sequence": "ATGGCCATTGTAATGGGCCGC"}
```
## Working with Public Databases
### Fetch and Analyze a Gene
```
1. Fetch from GenBank
Tool: fetch_genbank
Input: {
"accession": "NM_000207",
"email": "your@email.com"
}
2. Extract sequence from the result and translate
Tool: translate_sequence
Input: {"sequence": "<sequence from step 1>"}
```
### Search PubMed for Research
```
Tool: search_pubmed
Input: {
"query": "BRCA1 mutation cancer",
"max_results": 5,
"email": "your@email.com"
}
```
## Sequence Alignment Workflows
### Compare Two Sequences
```
1. Global alignment
Tool: pairwise_align
Input: {
"seq1": "ATGGCCATTGTAATGGGCCGC",
"seq2": "ATGGCCATTGTTATGGGCCGC",
"mode": "global"
}
2. Local alignment for finding similar regions
Tool: pairwise_align
Input: {
"seq1": "ATGGCCATTGTAATGGGCCGC",
"seq2": "ATGGCCATTGTTATGGGCCGC",
"mode": "local"
}
```
## Protein Structure Analysis
### Analyze PDB Structure
```
1. Fetch structure
Tool: fetch_pdb_structure
Input: {
"pdb_id": "1ABC",
"file_format": "pdb"
}
2. Calculate statistics
Tool: calculate_structure_stats
Input: {"pdb_file": "<path from step 1>"}
3. Analyze active site
Tool: find_active_site
Input: {
"pdb_file": "<path from step 1>",
"residue_numbers": [25, 50, 75],
"chain_id": "A"
}
```
## Phylogenetic Analysis
### Build Phylogenetic Tree
```
1. Prepare aligned sequences
sequences = [
"ATGGCCATTGTAATGGGCCGC",
"ATGGCCATTGTTATGGGCCGC",
"ATGGCCATTGTTAAGGGCCGC"
]
2. Build tree
Tool: build_phylogenetic_tree
Input: {
"sequences": sequences,
"method": "nj",
"labels": ["Species_A", "Species_B", "Species_C"]
}
3. Visualize tree
Tool: draw_tree
Input: {
"tree_newick": "<newick from step 2>",
"output_format": "ascii"
}
```
### Calculate Evolutionary Distances
```
Tool: calculate_distance_matrix
Input: {
"sequences": [
"ATGGCCATTGTAATGGGCCGC",
"ATGGCCATTGTTATGGGCCGC",
"ATGGCCATTGTTAAGGGCCGC"
],
"model": "identity",
"labels": ["Seq1", "Seq2", "Seq3"]
}
```
## Clinical Workflow Example
### Analyze Patient Sample
```
1. Search for gene information
Tool: search_pubmed
Input: {
"query": "TP53 mutation clinical significance",
"max_results": 10
}
2. Fetch reference sequence
Tool: fetch_genbank
Input: {
"accession": "NM_000546",
"email": "clinician@hospital.com"
}
3. Compare patient sequence to reference
Tool: pairwise_align
Input: {
"seq1": "<reference from step 2>",
"seq2": "<patient sequence>",
"mode": "global"
}
4. Translate both sequences
Tool: translate_sequence
Input: {"sequence": "<reference sequence>"}
Tool: translate_sequence
Input: {"sequence": "<patient sequence>"}
5. Identify mutations by comparing protein sequences
```
## Motif Analysis
### Find All Restriction Sites
```
# Find EcoRI sites (GAATTC)
Tool: find_motif
Input: {
"sequence": "ATGGAATTCGCCGAATTCTTA",
"motif": "GAATTC",
"overlapping": false
}
```
### Find Promoter Elements
```
# Find TATA box
Tool: find_motif
Input: {
"sequence": "<promoter sequence>",
"motif": "TATAAA",
"overlapping": true
}
```
## Working with UniProt
### Fetch and Analyze Protein
```
1. Fetch protein sequence
Tool: fetch_uniprot
Input: {
"uniprot_id": "P04637",
"format": "fasta"
}
2. Calculate properties
Tool: calculate_gc_content
Input: {"sequence": "<extracted sequence>"}
```
## Batch Processing
### Analyze Multiple Sequences
```
For each sequence in batch:
1. Calculate GC content
2. Find motifs
3. Translate to protein
4. Compare to reference
Use the tools in sequence for each sample.
```
## Tips
- Always validate sequences before complex operations
- Use appropriate email addresses for NCBI queries
- Cache PDB structures locally to avoid repeated downloads
- Consider rate limits when making multiple database queries
- Use local alignment for finding conserved regions
- Use global alignment for full sequence comparison
