Frameshift & In-Frame Stop Codon Detection

[leannehaggerty]

This process identifies coding transcripts with likely errors in their annotated open reading frames (ORFs). It looks for frameshifts (where the annotated coding sequence length is not a multiple of three) and premature stop codons that might indicate misannotation or pseudogene status. The method scans each annotated transcript’s coding sequence (CDS) to confirm that it starts with a canonical start codon (if expected), has a valid in-frame length, and ends with a valid stop codon. Suspicious transcripts (those with out-of-frame segments or unexpected stop codons) are flagged for manual review. Report (but not necessarily penalise) frameshifts rescued by shifting back to the original frame.