title: Automated alignment of RNA sequences to pseudoknotted structures.
abstract: 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.
authors.affiliation: Dept. of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder 80309-0347, USA. jtabaska@ural.colorado.edu
authors.forename: J E
authors.initials: JE
authors.lastname: Tabaska
authors.forename: G D
authors.initials: GD
authors.lastname: Stormo
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics*; D012342:RNA, Small Nuclear / Q000737:chemistry / Q000235:genetics; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics; D018894:Reverse Transcriptase Inhibitors / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods* / Q000706:statistics & numerical data; D012984:Software
chemical_list: D012342:RNA, Small Nuclear; D018894:Reverse Transcriptase Inhibitors; D012313:RNA; D012343:RNA, Transfer