Predicting reliable regions in protein sequence alignments

MOTIVATION Protein sequence alignments have a myriad of applications in bioinformatics, including secondary and tertiary structure prediction, homology modeling, and phylogeny. Unfortunately, all alignment methods make mistakes, and mistakes in alignments often yield mistakes in their application. Thus, a method to identify and remove suspect alignment positions could benefit many areas in protein sequence analysis. RESULTS We tested four predictors of alignment position reliability, including near-optimal alignment information, column score, and secondary structural information. We validated each predictor against a large library of alignments, removing positions predicted as unreliable. Near-optimal alignment information was the best predictor, removing 70% of the substantially-misaligned positions and 58% of the over-aligned positions, while retaining 86% of those aligned accurately.