bio-restriction-fragment-analysis
Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform double digests. Use when analyzing restriction digest fragment patterns.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bioskills__restriction-analysis__fragment-analysis --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BioPython 1.83+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Fragment Analysis **"Predict fragment sizes from a restriction digest"** → Simulate enzyme digestion to get fragment lengths, sequences, and gel electrophoresis patterns including double digests. - Python: `Bio.Restriction` analysis with `catalyze()` for fragment details ## Get Fragment Sizes ```python from Bio import SeqIO from Bio.Restriction import EcoRI record = SeqIO.read('sequence.fasta', 'fasta') seq = record.seq # catalyze() returns tuple: (fragments_5prime, fragments_3prime) # For standard use, take the first element fragments = EcoRI.catalyze(seq)[0] # fragments is tuple of Seq objects sizes = [len(f) for f in fragments] print(f'Fragment sizes: {sorted(sizes, reverse=True)}') ``` ## Linear vs Circular Digestion ```python from Bio.Restriction import EcoRI # Linear DNA fragments_linear
- Version Compatibility
- Get Fragment Sizes
- Linear vs Circular Digestion
- Get Fragment Sequences
- Double Digest
- Calculate Fragment Sizes from Positions
- Simulate Gel Pattern
- Detailed Fragment Report
- Compare Expected vs Observed Fragments
- Fragment with Sequence Context
- Notes
- Related Skills
What does the bio-restriction-fragment-analysis skill do?
Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform double digests. Use when analyzing restriction digest fragment patterns.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bioskills__restriction-analysis__fragment-analysis --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.