Seq7 is a new program for generating multiple structure-based alignments of RNA sequences. By using a variant of Dijkstra's algorithm to find the shortest path through a specially constructed graph, Seq7 is able to align RNA sequences to pseudoknotted structures in polynomial time. In this paper, we describe the operation of Seq7 and demonstrate the program's abilities. We also describe the use of Seq7 in an Expectation-Maximization procedure that automates the process of structural modeling and alignment of RNA sequences.

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