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Nucleic Acids Res. 2009 Jan;37(Database issue):D127-35. doi: 10.1093/nar/gkn806. Epub 2008 Nov 6.

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

Author information

1
Department of Computer and Information Sciences, University of Delaware, Newark, Delaware 19716, USA. taufer@udel.edu

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.

PMID:
18988624
PMCID:
PMC2686561
DOI:
10.1093/nar/gkn806
[Indexed for MEDLINE]
Free PMC Article

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