sequence-alignment
Trigger when user needs to align DNA/protein sequences, compare biological sequences, search for similar sequences in databases, or perform BLAST-based similarity analysis. Use for bioinformatics sequence comparison tasks.
Install with Tessl CLI
npx tessl i github:aipoch/medical-research-skills --skill sequence-alignment84
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Sequence Alignment
A skill for performing sequence alignment using NCBI BLAST API. Supports nucleotide and protein sequence comparison against major biological databases.
Features
- BLAST API Integration: Query NCBI BLAST service for sequence similarity search
- Multiple BLAST Programs: blastn, blastp, blastx, tblastn, tblastx
- Alignment Visualization: Display results in human-readable format
- Database Support: nr, nt, swissprot, refseq, pdb, and more
Usage
python scripts/main.py --sequence "ATGCGTACGTAGCTAGCTAG" --program blastn --database nt --output results.txtParameters
| Parameter | Description | Required |
|---|---|---|
--sequence | Query sequence (DNA/Protein) | Yes |
--program | BLAST program: blastn, blastp, blastx, tblastn, tblastx | Yes |
--database | Target database: nr, nt, swissprot, pdb, refseq_protein | Yes |
--output | Output file path | No |
--format | Output format: text, json, csv | No (default: text) |
--max_hits | Maximum number of hits to return | No (default: 10) |
--evalue | E-value threshold | No (default: 10) |
Technical Difficulty
Medium - Requires understanding of BLAST algorithm, API handling with retry logic, and biological sequence formats.
BLAST Programs Reference
| Program | Query Type | Database Type | Use Case |
|---|---|---|---|
| blastn | Nucleotide | Nucleotide | DNA vs DNA |
| blastp | Protein | Protein | Protein vs Protein |
| blastx | Nucleotide (translated) | Protein | DNA vs Protein |
| tblastn | Protein | Nucleotide (translated) | Protein vs DNA |
| tblastx | Nucleotide (translated) | Nucleotide (translated) | Translated DNA vs DNA |
Example Workflows
DNA Sequence Similarity Search
python scripts/main.py --sequence "ATGGCCCTGTGGATGCGCTTCTTAGTCG" --program blastn --database nt --max_hits 5Protein Sequence Alignment
python scripts/main.py --sequence "MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGT" --program blastp --database swissprot --evalue 0.001Output Format
Results include:
- Query sequence info
- Hit definitions and accession numbers
- Alignment scores (bit score, e-value)
- Percent identity and similarity
- Alignment visualization with match/mismatch highlighting
References
Risk Assessment
| Risk Indicator | Assessment | Level |
|---|---|---|
| Code Execution | Python scripts with tools | High |
| Network Access | External API calls | High |
| File System Access | Read/write data | Medium |
| Instruction Tampering | Standard prompt guidelines | Low |
| Data Exposure | Data handled securely | Medium |
Security Checklist
- No hardcoded credentials or API keys
- No unauthorized file system access (../)
- Output does not expose sensitive information
- Prompt injection protections in place
- API requests use HTTPS only
- Input validated against allowed patterns
- API timeout and retry mechanisms implemented
- Output directory restricted to workspace
- Script execution in sandboxed environment
- Error messages sanitized (no internal paths exposed)
- Dependencies audited
- No exposure of internal service architecture
Prerequisites
No additional Python packages required.
Evaluation Criteria
Success Metrics
- Successfully executes main functionality
- Output meets quality standards
- Handles edge cases gracefully
- Performance is acceptable
Test Cases
- Basic Functionality: Standard input → Expected output
- Edge Case: Invalid input → Graceful error handling
- Performance: Large dataset → Acceptable processing time
Lifecycle Status
- Current Stage: Draft
- Next Review Date: 2026-03-06
- Known Issues: None
- Planned Improvements:
- Performance optimization
- Additional feature support
- Repository
- aipoch/medical-research-skills
- Commit
f11484c
- Last updated
- Created
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