biopython

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 multi-service integration use bioservices.

1.17x

Quality

75%

Does it follow best practices?

Impact

96%

1.17x

Average score across 3 eval scenarios

Securityby

Advisory

Suggest reviewing before use

Optimize this skill with Tessl

npx tessl skill review --optimize ./scientific-skills/biopython/SKILL.md

Evaluation results

90%

19%

Gene Analysis Pipeline for Chloroplast Research

Batch Entrez sequence retrieval and analysis

Criteria

Without context

With context

Entrez email set

100%

Handles closed

80%

100%

gc_fraction used

100%

ProteinAnalysis used

100%

Sequences cached locally

100%

Network error handling

results.csv produced

75%

100%

Lowercase format strings

100%

uv pip install used

100%

Iterator-based parsing

100%

10%

Evolutionary Analysis of a Conserved Protein Family

Phylogenetic tree construction from protein alignment

Criteria

Without context

With context

No deprecated pairwise2

100%

PairwiseAligner used

100%

BLOSUM62 matrix

100%

DistanceCalculator used

100%

DistanceTreeConstructor used

100%

Tree rooted

100%

Newick file written

100%

ASCII visualization output

100%

AlignIO lowercase format

100%

distance_matrix.csv produced

100%

13%

Structural Analysis of a Protein Binding Region

PDB structure hierarchy navigation and spatial analysis

Criteria

Without context

With context

QUIET=True parser

100%

mmCIF or PDB format

100%

SMCRA hierarchy — model access

100%

SMCRA hierarchy — chain access

100%

SMCRA hierarchy — residue/atom access

100%

NeighborSearch used

100%

Atom distance calculation

58%

100%

structure_summary.txt present

100%

neighbors.csv present

100%

uv pip install used

100%

Structure cached locally

100%

Repository: K-Dense-AI/claude-scientific-skills
Commit: b58ad7e

Evaluated: 27 days ago
Agent: Claude Code
Model: Claude Sonnet 4.6

Table of Contents

Gene Analysis Pipeline for Chloroplast Research Evolutionary Analysis of a Conserved Protein Family Structural Analysis of a Protein Binding Region

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