High throughput retrieval of secondary structure annotation for proteins & RNA

Since mid-2025, PFAM no longer include secondary structure annotation in their Stockholm files, only 'pAS' active site annotations. This means the only way people can get secondary structure annotations for their (protein) sequences is currently to run JPred, or retrieve 3D structure data (be it predicted or observed). Neither route is practical when working with alignments of thousands of sequences with Jalview's current web services.