Multiple alignment through protein secondary-structure information

It is well known that protein secondary structure information can help the process of performing multiple align- ment, in particular when the amount of similarity among the involved sequences moves towards the “twilight zone” (less than 30% of pairwise similarity). In this paper, a multiple alignment algorithm is presented, explicitly designed for exploiting any available secondary structure information. A layered architecture with two interacting levels has been defined for dealing with both primary and secondary structure information of target sequences. Secondary structure (either available or predicted by resorting to a technique based on multiple experts) is used to calculate an initial alignment at the secondary level, to be arranged by locally- scoped operators devised to refine the alignment at the primary level. Aimed at evaluating the impact of secondary information on the quality of alignments, in particular alignments with a low degree of similarity, the technique has been implemented and assessed on relevant test cases.