Automated Alignment of RNA Sequences to Pseudoknotted Structures

Proceedings Of The Fifth International Conference On Intelligent Systems For Molecular Biology

Volume

Proceedings Of The Fifth International Conference On Intelligent Systems For Molecular Biology

Contents

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 Sex/7 in an Expectation-Maximization procedure that automates the process of structural modeling and alignment of RNA sequences.