An extension of PseudoBase for easy searching, formatting and visualization of pseudoknots. PseudoBase++ 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.
Department of Computer and Information Sciences, University of Delaware, Newark, Delaware; Department of Computer Science; Bioinformatics Program; Border Biomedical Research Center, The University of Texas at El Paso, USA; Section Theoretical Biology, Leiden Institute of Biology; Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands; Department of Mathematical Sciences, The University of Texas at El Paso, El Paso, TX, USA
PseudoBase++ funding source(s)
Texas Advanced Research Program (003661-0008-2006, 003661-0013-2007); the National Institutes of Health (S06GM08012-38, 5G12RR008124-11, 3T34GM008048-20S1); the National Science Foundation (DMS0800272); the CRA-W Distributed Research Experiences for Undergraduates Program 2008