• fold recognition;
  • profile–profile alignment;
  • homology detection;
  • sequence alignments


To improve the detection of related proteins, it is often useful to include evolutionary information for both the query and target proteins. One method to include this information is by the use of profile–profile alignments, where a profile from the query protein is compared with the profiles from the target proteins. Profile–profile alignments can be implemented in several fundamentally different ways. The similarity between two positions can be calculated using a dot-product, a probabilistic model, or an information theoretical measure. Here, we present a large-scale comparison of different profile–profile alignment methods. We show that the profile–profile methods perform at least 30% better than standard sequence-profile methods both in their ability to recognize superfamily-related proteins and in the quality of the obtained alignments. Although the performance of all methods is quite similar, profile–profile methods that use a probabilistic scoring function have an advantage as they can create good alignments and show a good fold recognition capacity using the same gap-penalties, while the other methods need to use different parameters to obtain comparable performances. Proteins 2004. © 2004 Wiley-Liss, Inc.