title: PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots.
abstract: Pseudoknots have been recognized to be an important type of RNA secondary structures responsible for many biological functions. PseudoBase, a widely used database of pseudoknot secondary structures developed at Leiden University, contains over 250 records of pseudoknots obtained in the past 25 years through crystallography, NMR, mutational experiments and sequence comparisons. To promptly address the growing analysis requests of the researchers on RNA structures and bring together information from multiple sources across the Internet to a single platform, we designed and implemented PseudoBase++, an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots. PseudoBase++ (http://pseudobaseplusplus.utep.edu) maps the PseudoBase dataset into a searchable relational database including additional functionalities such as pseudoknot type. PseudoBase++ links each pseudoknot in PseudoBase to the GenBank record of the corresponding nucleotide sequence and allows scientists to automatically visualize RNA secondary structures with PseudoViewer. It also includes the capabilities of fine-grained reference searching and collecting new pseudoknot information.
authors.affiliation: Department of Computer and Information Sciences, University of Delaware, Newark, Delaware 19716, USA. taufer@udel.edu
authors.forename: Michela
authors.initials: M
authors.lastname: Taufer
authors.forename: Abel
authors.initials: A
authors.lastname: Licon
authors.forename: Roberto
authors.initials: R
authors.lastname: Araiza
authors.forename: David
authors.initials: D
authors.lastname: Mireles
authors.forename: F H D
authors.initials: FH
authors.lastname: van Batenburg
authors.forename: Alexander P
authors.initials: AP
authors.lastname: Gultyaev
authors.forename: Ming-Ying
authors.initials: MY
authors.lastname: Leung
mesh_terms: D020029:Base Pairing; D003196:Computer Graphics; D030561:Databases, Nucleic Acid; D012313:RNA / Q000737:chemistry*; D018511:Systems Integration
chemical_list: D012313:RNA