biopython-sequence-analysis
Facilitates comprehensive sequence analysis in bioinformatics, enabling parsing, alignment, and phylogenetic tree construction.
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Security score
The biopython-sequence-analysis skill was audited on May 24, 2026 and we found 11 security issues across 2 threat categories, including 1 high-severity. Review the findings below before installing.
Categories Tested
Security Issues
medium line 262
Python subprocess execution
SourceSKILL.md
| 262 | subprocess.run( |
medium line 268
Python subprocess execution
SourceSKILL.md
| 268 | result = subprocess.run( |
medium line 459
Python subprocess execution
SourceSKILL.md
| 459 | subprocess.run( |
high line 767
Python subprocess execution
SourceSKILL.md
| 767 | | `Bio.Application.ApplicationError: blastall not found` | Legacy `blastall` replaced by BLAST+ | Replace `NcbiblastpCommandline` with `subprocess.run(["blastp", ...])` and BLAST+ tools | |
low line 32
External URL reference
SourceSKILL.md
| 32 | - **NCBI access**: Set `Entrez.email` before any E-utilities call; obtain a free API key at https://www.ncbi.nlm.nih.gov/account/ for 10 req/s (default is 3 req/s) |
low line 615
External URL reference
SourceSKILL.md
| 615 | Entrez.api_key = "YOUR_API_KEY" # from https://www.ncbi.nlm.nih.gov/account/ |
low line 765
External URL reference
SourceSKILL.md
| 765 | | `urllib.error.HTTPError: 429 Too Many Requests` | Exceeding NCBI rate limit (3 req/s) | Add `time.sleep(0.4)` between calls, or register a free API key at https://www.ncbi.nlm.nih.gov/account/ for 1 |
low line 785
External URL reference
SourceSKILL.md
| 785 | - [Biopython Tutorial and Cookbook](https://biopython.org/DIST/docs/tutorial/Tutorial.html) — comprehensive official tutorial (Chapters 2, 5, 6, 7, 9, 11) |
low line 786
External URL reference
SourceSKILL.md
| 786 | - [Biopython API Reference](https://biopython.org/docs/latest/api/) — complete module and class documentation |
low line 788
External URL reference
SourceSKILL.md
| 788 | - [NCBI E-utilities Documentation](https://www.ncbi.nlm.nih.gov/books/NBK25499/) — Entrez API reference for esearch, efetch, elink, esummary |
low line 789
External URL reference
SourceSKILL.md
| 789 | - [PairwiseAligner Migration Guide](https://biopython.org/docs/latest/api/Bio.Align.html) — replacing the deprecated `Bio.pairwise2` module |
Scanned on May 24, 2026
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Categorydata analytics
UpdatedJune 15, 2026
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