Abstract: The invention relates to a method for annotating protein sequences consistently, using disparate secondary database protein family information. In the method, information relating to the family to which a protein belongs is derived from two or more secondary databases (2DBs), each 2DB being generated by a different modelling approach and wherein at least one 2DB provides no single alignment of protein sequences in each family. The method involves the steps of extracting protein family information from said at least two 2DBs; and incorporating this information into a single modelling infrastructure.