GenBank & FASTA Nucleotide Sequences (.gb, .gbk, .fasta, .fa)

@modelscript/genbank (languages/genbank) provides native WebAssembly GLR parsing, NCBI genetic code translation verification, 6-frame Open Reading Frame (ORF) discovery, restriction endonuclease digestion mapping, Codon Adaptation Index ($\text{CAI}$) calculation, DAEBuilder transcriptional/translational lowering, and SBOL3 / Modelica projections for NCBI GenBank and FASTA plasmid, viral, and genomic sequence files.

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Supported Extensions & Standards

Extension	Format	Description
.gb, .gbk, .genbank	NCBI GenBank Flat File	Annotated nucleotide sequence record (LOCUS, DEFINITION, ACCESSION, FEATURES, ORIGIN, //)
.fasta, .fa, .fna	FASTA Sequence	Multi-sequence nucleotide or peptide FASTA records (>header)

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Key Capabilities

1. Annotated Feature Tables & Location Operators

• Parses LOCUS topology (linear / circular), molecular type (DNA, RNA, mRNA), and FEATURES annotations (CDS, promoter, RBS, terminator, gene, rep_origin, misc_feature) with complement(...), join(...), and /translation qualifiers.

2. Sequence Analysis, ORFs, Restriction Maps & CAI

• 6-Frame ORF Finder: Identifies start (ATG, GTG, TTG) to stop (TAA, TAG, TGA) open reading frames across forward and reverse-complement strands.
• Restriction Enzyme Mapper: Computes cleavage coordinates and fragment lengths for common Type II endonucleases (EcoRI, BamHI, HindIII, NotI, XbaI, SpeI, PstI, BsaI).
• GC Content, Melting Temperature ($T_m$) & CAI: Evaluates GC fraction, primer $T_m$, and E. coli / mammalian codon usage bias.

3. SBOL3, Modelica & DAE Lowering

• Projects annotated CDS, promoter, RBS, and terminator features into SBOL3 genetic circuit components (genbankToSbol), Modelica 3.x gene expression ODEs (genbankToModelica), and @modelscript/runtime's DAEBuilder.

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Pre-Flight Diagnostics

10 rules8 error2 warning

Code	Rule	Severity	Message
M9351	locus-length-mismatch	error	LOCUS '<locus>' declares length '<declaredLength>' bp, but ORIGIN sequence has '<actualLength>' bp.
M9352	invalid-sequence-character	error	Sequence '<locus>' contains non-IUPAC character '<invalidChar>' at position '<position>'.
M9353	feature-location-out-of-bounds	error	Feature '<featureName>' location '[<start>..<end>]' is out of bounds for sequence '<locus>' of length '<seqLength>' bp.
M9354	cds-missing-start-codon	warning	Coding sequence (CDS) '<cdsName>' begins with '<actualCodon>' instead of a valid start codon ('ATG', 'GTG', or 'TTG').
M9355	cds-missing-stop-codon	warning	Coding sequence (CDS) '<cdsName>' ends with '<actualCodon>' instead of a valid stop codon ('TAA', 'TAG', or 'TGA').
M9356	cds-internal-premature-stop	error	Coding sequence (CDS) '<cdsName>' contains an internal premature stop codon '<stopCodon>' at codon '<codonIndex>'.
M9357	cds-translation-mismatch	error	Coding sequence (CDS) '<cdsName>' /translation qualifier '<actualTranslation>' does not match translated sequence '<expectedTranslation>'.
M9358	empty-genbank-origin	error	GenBank record '<locus>' has an empty or missing ORIGIN nucleotide sequence.
M9359	inverted-feature-span	error	Feature '<featureName>' in non-circular sequence '<locus>' has inverted span '[<start>..<end>]' ('start > end').
M9360	duplicate-locus-identifier	error	LOCUS or FASTA identifier '<locus>' is declared multiple times in the document.

Generated from languages/genbank/src/errors.ts. All languages →

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CLI Usage

# Validate LOCUS length consistency, CDS frame divisibility, and translations
msx lint pUC19_Plasmid.gb

# Parse and inspect GenBank or FASTA records
msx parse pUC19_Plasmid.gb