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PseudoBase


NAR Molecular Biology Database Collection entry number 242
Batenburg, F.H.D. van1, Gultyaev, A.P.1, Pleij, C.W.A.2
1Group Theoretical Biology, Leiden University of Biology, Leiden University
2Leiden Institute of Chemistry, Leiden University

Database Description

PseudoBase is a database containing structural, functional and sequence data related to RNA pseudoknots. It can be reached by its central page at http://pseudobaseplusplus.utep.edu. From here one can retrieve pseudoknot data as well as submit data for pseudoknots that are not yet in the database. There are various alternatives to retrieve data, e.g. in a survey sorted alphabetically on organism names, or sorted on types of RNA molecules or on structural features (such as sizes of paired regions and loops). For each pseudoknot, thirteen items are stored: a PKB-number (a unique number for each pseudoknot entry), definition, organism, abbreviation, category (one of 13 alternatives), keywords, EMBL accession number of the sequence containing this pseudoknot, name of person that submitted the data, support that can be given regarding the reliability of the pseudoknot, reference(s) to relevant paper(s), sizes of each stem, sizes of each loop, the stem positions in the sequence, and finally a so-called bracket view that shows the base-pairs in the pseudoknotted region of the sequence. At the time of writing the database contains over 300 entries with classical H-type pseudoknots as well as more complicated ones.

Recent Developments

Based on PseudoBase, PseudoBase++ 3 (http://pseudobaseplusplus.utep.edu) is a a searchable, up-to-date database of the PseudoBase pseudoknots, wrapped by a versatile, user-friendly interface that provides scientists with a powerful engine to access PseudoBase. Among its several functionalities, PseudoBase++ allows for efficient compound searches; extracts sequences in FASTA, dot-parentheses, and BPSEQ formats to be used for prediction algorithms; automates visualization of structures through PseudoViewer; and provides Web services to directly access the database.

References

1. van Batenburg, F.H.D., Gultyaev, A.P., and Pleij, C.W.A.(2001) PseudoBase: structural information on RNA pseudoknots. Nucleic Acids Res., 29(1), 194-195.
2. van Batenburg, F.H.D., Gultyaev, A.P., Pleij, C.W.A., Ng, J., and Oliehoek, J. (2000) PseudoBase: a database with RNA pseudoknots. Nucleic Acids Res., 28, 201-204.
3. Taufer, M., Licon, A., Araiza, R., Mireles, D., van Batenburg, F.H.D., Gultyaev, A.P., and Leung, M.-Y. (2008) PseudoBase++: An Extension of PseudoBase for Easy Searching, Formatting, and Visualization of Pseudoknots, Nucleic Acids Res., 37, D127-D135.


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