A study on protein sequence alignment quality

One of the most central methods in bioinformatics is the alignment of two protein or DNA sequences. However, so far large‐scale benchmarks examining the quality of these alignments are scarce. On the other hand, recently several large‐scale studies of the capacity of different methods to identify related sequences has led to new insights about the performance of fold recognition methods. To increase our understanding about fold recognition methods, we present a large‐scale benchmark of alignment quality. We compare alignments from several different alignment methods, including sequence alignments, hidden Markov models, PSI‐BLAST, CLUSTALW, and threading methods. For most methods, the alignment quality increases significantly at about 20% sequence identity. The difference in alignment quality between different methods is quite small, and the main difference can be seen at the exact positioning of the sharp rise in alignment quality, that is, around 15–20% sequence identity. The alignments are improved by using structural information. In general, the best alignments are obtained by methods that use predicted secondary structure information and sequence profiles obtained from PSI‐BLAST. One interesting observation is that for different pairs many different methods create the best alignments. This finding implies that if a method that could select the best alignment method for each pair existed, a significant improvement of the alignment quality could be gained. Proteins 2002;46:330–339. © 2002 Wiley‐Liss, Inc.