Construct QC linter
construct_qcLint a coding DNA sequence for premature stops, internal RBS/polyA motifs, unwanted restriction sites, GC extremes and repeats.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| gcLow | No | GC% below this flags an AT-rich window. | |
| gcHigh | No | GC% above this flags a GC-rich window. | |
| gcWindow | No | Sliding-window size (nt) for GC-extreme scanning. | |
| sequence | Yes | Nucleotide sequence (raw or FASTA; IUPAC accepted). | |
| frameStart | No | 1-based nucleotide where the reading frame begins. | |
| avoidEnzymes | No | Enzyme names whose internal sites should be flagged as errors. Matched against the curated common-enzyme set plus the Golden Gate Type IIS enzymes (BsaI, BbsI, Esp3I/BsmBI); an unrecognised name is rejected, never skipped. | |
| homopolymerMin | No | Minimum run length to flag a homopolymer. | |
| crypticOrfMinAa | No | Minimum peptide length (aa) for a hidden alternate-frame ORF to be flagged. |