Evaluations of protein sequence alignments using structural information

Correct alignment of protein sequences is critical for accurate understanding of the evolution of the protein. Therefore, it is important to know how likely an alignment is correct. Any approach that uses randomized sequences to access significance uses only part of the information inherent in an amino acid sequence. Offset alignment evaluation is a method to model and estimate the confidence of a given protein sequence alignment, which takes into account the inherent information from the protein sequence secondary structures. The confidence of a given alignment is estimated by a significance score based on the set of offset alignments. Finally, we introduce OAE, a Java implementation of the Offset alignment evaluation, which is freely available to the public.