Hey! I've been updating #C084HP11VPF lately and I want to make sure there is no overlap with funcscan. Currently, proteinannotator takes only amino acid sequence inputs (not nucleotide), and we might allow optional inputs such as protein structures (and then using foldseek to annotate, finding distant homologs) and maybe genomic context in the future. For now, on the dev branch, we allow downloading HMM libraries such as Pfam and FunFam and usin hmmsearch with the input proteins to identify matching domains. We also predict potential secondary structures with

s4pred

.