Design from GenBank or SnapGene

Annotated mode is useful for plasmids and constructs because existing labels can define required intervals and remain visible in output.

Default required_interval

The example GenBank file contains a feature labeled required_interval:

smfprimer design annotated docs/examples/annotated_construct.gb \
  --workflow conversion \
  --product-size 50:100 \
  --min-tm 30 \
  --optimum-tm 50 \
  --max-tm 80 \
  --output annotated_primers.tsv

The companion annotated_primers.gb retains the original example_promoter and required_interval features and adds ranked amplicon and primer features.

Select custom feature names

Repeat the option to design around several labels:

smfprimer design annotated construct.dna \
  --required-feature promoter_A \
  --required-feature enhancer_B \
  --product-size 300:700 \
  --output construct_primers.tsv

Or provide one label per line:

smfprimer design annotated construct.gb \
  --required-features-file docs/examples/required_features.txt \
  --output construct_primers.tsv

Each matching feature becomes a separate target. SnapGene .dna files are accepted as input; the companion annotation file is GenBank because Biopython does not provide a maintained SnapGene writer.

Warning

Required features that cross the origin of a circular construct are not currently supported. Represent the desired target as one contiguous span.