Automated Alignment of RNA Sequences to Pseudoknotted Structures

Seq7 is a newprogramfor generating multiple structure-based alignments of RNAsequences. Byusing a variant of Dijkstra’s algorithm to find the shortest path through a specially constructed graph, Seq7 is able to align RNAsequences to pseudoknotted structures in polynomial time. In this paper, we describe the operation of Seq7 and demonstrate the program’s abilities. Wealso describe the use of Sex/7 in an Expectation-Maximizationprocedure that automates the process of structural modelingand alignment of RNAsequences.

• Type: Conference
• Year: 1997
• Where: ISMB
• Authors: Jack E. Tabaska, Gary D. Stormo
• Keywords: Computational Biology, ISMB 1997, Multiple Structure-based Alignments, Shortest Path, Structural Modelingand Alignment