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Nucleic Acids Research Advance Access published online on November 6, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn806
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots

Michela Taufer1,*, Abel Licon1, Roberto Araiza2,3,4, David Mireles2, F. H. D. van Batenburg5, Alexander P. Gultyaev5,6 and Ming-Ying Leung3,4,7

1Department of Computer and Information Sciences, University of Delaware, Newark, Delaware 19716, 2Department of Computer Science, 3Bioinformatics Program, 4Border Biomedical Research Center, The University of Texas at El Paso, USA, 5Section Theoretical Biology, Leiden Institute of Biology, 6Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300RA Leiden, The Netherlands and 7Department of Mathematical Sciences, The University of Texas at El Paso, El Paso, Texas 79968, USA

*To whom correspondence should be addressed. Tel: +13028310071; Fax: +13028318458; Email: taufer{at}udel.edu

Received September 15, 2008. Revised October 9, 2008. Accepted October 10, 2008.

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.


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