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Nucleic Acids Research, 2000, Vol. 28, No. 1 201-204
© 2000 Oxford University Press

PseudoBase: a database with RNA pseudoknots

F. H. D. van Batenburg1,*, A. P. Gultyaev1,2, C. W. A. Pleij2, J. Ng1 and J. Oliehoek1

1Group Theoretical Biology and Phylogenetics, Institute of Evolutionary and Ecological Sciences, Leiden University, Kaiserstraat 63, 2311GP Leiden, The Netherlands and 2Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300RA Leiden, The Netherlands

PseudoBase is a database containing structural, functional and sequence data related to RNA pseudo­knots. It can be reached at http://wwwbio.Leiden Univ.nl/~Batenburg/PKB.html . This page will direct the user to a retrieval page from where a particular pseudoknot can be chosen, or to a submission page which enables the user to add pseudoknot information to the database or to an informative page that elaborates on the various aspects of the database. For each pseudoknot, 12 items are stored, e.g. the nucleotides of the region that contains the pseudoknot, the stem positions of the pseudoknot, the EMBL accession number of the sequence that contains this pseudoknot and the support that can be given regarding the reliability of the pseudoknot. Access is via a small number of steps, using 16 different categories. The development process was done by applying the evolutionary methodology for software development rather than by applying the methodology of the classical waterfall model or the more modern spiral model.

* To whom correspondence should be addressed. Tel: +31 71 527 4972; Fax: +31 71 527 4900; Email: batenburg@rulsfb.leidenuniv.nl


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