A major stumbling block of manual approaches is the problem of keeping the alignments up to date with new releases of protein and efficient updating scheme is required to ensure stabil- ity of the database. These requirements are met in Pfam by using two alignments: a high quality seed alignment, which changes only little or not at all between releases, and a full alignment, which is built by automatically aligning all members to a hidden Markov model-based profile (HMM) derived from the seed alignment. The method that generates the best full alignment may vary slightly for differ- ent families, so the parameters used are stored for reproducibility. This split into seed/full is.
