Unfortunately, considering structural information adds an additional level of complexity to the problem of aligning two or several sequences. In the remainder of this section, we present a classification of structural alignment problem variants including previous work. Section 2 describes our new approach to multiple sequence-structure alignment. We employ methods from mathematical programming and solve the problem as an integer linear program resulting from a graph-theoretical reformulation. Section 3 is dedicated to an extensive computational study. We describe LARA, the freely available implementation of our novel approach, and present detailed results of a comparative study including state-of-the-art programs on a recently published benchmark database of structural alignments. The results show that on average our software is currently the best program in terms of alignment quality, outperforming other programs with an increasing number of input sequences. Finally, we discuss our results and suggest future research directions in Sect. 4.
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