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.

Abstract: The invention relates to a method of aligning a plurality of sequences. In a similar way to known multiple alignment methods, the method of the invention uses a profile for the nominated sequence in an alignment strategy. The key novel concept behind the method of the invention is to allow the profile to be extended in regions where gaps are desired. This alternative strategy is implemented using pre-generated profiles as a basis for the multiple alignment.

Abstract: The invention relates to a method for reducing the number of results generated by the alignment of a query protein or nucleotide sequence against a target protein or nucleotide sequence by an alignment algorithm, the method comprising the step of combining two or more alignment results into a single alignment result for each specific region of sequence alignment identified between query and target sequences.

Abstract: The invention concerns methods and systems for predicting the function of proteins. In particular, the invention relates to databases in which details of sequence homologies, biological functions and structures that are shared between proteins of differing sequence have been compiled. The invention also relates to methods, systems and computer software that allows the prediction of protein function and structure and, optionally, the ligand binding properties of the proteins within such a database.