title: Alignment editing and identification of consensus secondary structures for nucleic acid sequences: interactive use of dot matrix representations.
abstract: We present a computer-aided approach for identifying and aligning consensus secondary structure within a set of functionally related oligonucleotide sequences aligned by sequence. The method relies on visualization of secondary structure using a generalization of the dot matrix representation appropriate for consensus sequence data sets. An interactive computer program implementing such a visualization of consensus structure has been developed. The program allows for alignment editing, data and display filtering and various modes of base pair representation, including co-variation. The utility of this approach is demonstrated with four sample data sets derived from in vitro selection experiments and one data set comprising tRNA sequences.
authors.affiliation: NeXstar Pharmaceuticals Inc. Boulder, CO 80301, USA.
authors.forename: J P
authors.initials: JP
authors.lastname: Davis
authors.forename: N
authors.initials: N
authors.lastname: Janjić
authors.forename: D
authors.initials: D
authors.lastname: Pribnow
authors.forename: D A
authors.initials: DA
authors.lastname: Zichi
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D003198:Computer Simulation; D016384:Consensus Sequence; D003626:Data Display; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*
chemical_list: D009843:Oligoribonucleotides; D012313:RNA