How do I create an intron-containing feature based on alignment of a cDNA sequence with a reference genomic sequence?
Align a cDNA to a Reference Sequence
Open a reference genomic DNA sequence, then import and align your cDNA by clicking Tools → Align to Reference DNA Sequence.
In Map view, SnapGene will show the alignment, with gaps inserted if appropriate.
- In Map view or Sequence view select the aligned sequence in the list.
- Click the dropdown Aligned Sequences → Make Feature from Sequence.
Alternatively, right-click (Windows) or Ctrl-click (macOS) on the cDNA sequence name and choose Make Feature from Selected Sequence.
Choose to Annotate Gaps as Introns
Set the minimum gap size to be considered an intron then click Annotate Gaps.
A new feature of type misc_feature will be created with gaps between the aligned regions. The gaps will correspond to introns†.
Save to retain the new feature.
† Note the exon/intron boundaries based on alignment are not guaranteed to match true splice sites. You should double check the boundaries and adjust if required based on known splice motifs for the source organism.