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Parse SnapGene .dna files. Use when the user asks to read, convert, or extract information from SnapGene files, or needs to convert .dna to GenBank/FASTA format.
Codex または Claude でインストール この Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。
SOC 職業分類に基づく
Predict optimal construct boundaries for protein expression. Use when the user asks about domain boundaries, construct design, truncations, which region of a protein to express, or identifying disordered regions.
Manage lab notebook entries, registry items (plasmids, proteins, etc.), templates, widgets, and audit logs via the Labbook service. Use when creating or viewing lab notebook entries, managing the sample registry, or documenting experiments.
Verify open reading frames (ORFs) in plasmid sequences. Use when the user asks about verifying protein coding sequences, checking if an ORF is present in a plasmid, finding where a protein is encoded, or doing six-frame translation analysis.
Fetch sequencing data from Plasmidsaurus. Use when the user asks about listing sequencing orders, downloading sequencing results, checking order status, or retrieving plasmid sequences from Plasmidsaurus.
Design PCR primers for molecular cloning. Use when the user asks about designing primers, LIC cloning primers, sequencing primers, Gibson assembly primers, or working with NCBI accession codes for cloning.
Calculate protein parameters (MW, pI, extinction coefficient) and generate purification recommendations. Use when the user asks about protein properties, molecular weight, isoelectric point, extinction coefficients, or purification strategies.
| name | snapgene |
| description | Parse SnapGene .dna files. Use when the user asks to read, convert, or extract information from SnapGene files, or needs to convert .dna to GenBank/FASTA format. |
Parse SnapGene .dna files and extract sequence, features, and metadata.
scripts/snapgene_cli.py
pip install snapgene_reader biopython
python3 scripts/snapgene_cli.py 438-C.dna
Output: name, length, feature count, topology
python3 scripts/snapgene_cli.py 438-C.dna --features
Output: table of all features (type, position, strand, name)
python3 scripts/snapgene_cli.py 438-C.dna --sequence
Output: raw DNA sequence
python3 scripts/snapgene_cli.py 438-C.dna --export-gb 438-C.gb
python3 scripts/snapgene_cli.py 438-C.dna --export-fasta 438-C.fa
python3 scripts/snapgene_cli.py 438-C.dna --json
Output: full data as JSON (name, length, sequence, features with qualifiers)
| Option | Short | Description |
|---|---|---|
--features | -f | List all features as table |
--sequence | -s | Print DNA sequence only |
--export-gb FILE | -g | Export to GenBank format |
--export-fasta FILE | -a | Export to FASTA format |
--json | -j | Output as JSON |
SnapGene File: 438-C.dna
==================================================
Name: 438-C
Length: 6,847 bp
Features: 24
Topology: circular
Feature types:
CDS: 4
misc_feature: 8
promoter: 2
rep_origin: 1
terminator: 2
Type Start End Strand Name
------------------------------------------------------------
promoter 1 300 + polyhedrin promoter
CDS 500 2846 + His6-MBP-TEV
misc_feature 2847 2864 + LIC site
CDS 5000 5600 - GentR
Use with construct generator to load vectors:
from snapgene_reader import snapgene_file_to_seqrecord
record = snapgene_file_to_seqrecord("438-C.dna")
sequence = str(record.seq)
features = record.features
Use with orf_verifier for clone verification:
# Convert vector to GenBank first
python3 scripts/snapgene_cli.py vector.dna --export-gb vector.gb
# Then verify clone
python3 scripts/orf_verifier_cli.py verify-clone --expected vector.gb --sequencing clone.seq