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Pseudoknots

An RNA secondary structure is formed by base pairing between various regions in the RNA molecule, resulting in a configuration of double-helical regions (stems) and single-stranded loops. RNA pseudoknot is defined as a secondary structure formed by pairing between a loop and a region located outside (upstream or downstream) of the stem flanking the loop (see movie below). Pseudoknots have been implicated in important biological functions such as gene expression and viral genome replication [1,2].



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PseudoBase

PseudoBase [3] is currently the main public source of information about pseudoknot secondary structures. PseudoBase includes over 200 records of pseudoknots obtained in the past 25 years through crystallography, NMR, mutational experiments, and sequence comparisons.

PseudoBase++

PseudoBase++ [4] is a searchable up-to-date database of the PseudoBase pseudoknots wrapped by a versatile, user-friendly interface providing scientists with a powerful engine to access, search, select, and sort data based on different fine-grained criteria. The PseudoBase++ interface allows scientists to visualize selected structures with PseudoViewer [5], to map existing sequences to GenBank [6], and to insert new pseudoknots to the PseudoBase dataset through a syntax-controlled interface that prevents structural error for long sequences. PseudoBase++ is part of the RNAVLab project a virtual laboratory for the analysis of RNA secondary structures [7] and serves the specific purpose of facilitating analysis of pseudoknots.

References:

[1] Jones-Rhoades, M.W. et al. (2006) Annu Rev Plant Biol, 57, 19-53.

[2] Lyubetsky, V.A. et al. (2007) J Bioinform Comput Biol., 5(1), 155-80.

[3] Van Batenburg, F.H.D. et al. (2000) Nucleic Acids Res., 28(1), 201-204.

[4] Taufer, M. et al. (2009) Nucleic Acids Research. Database Issue, Volume 37, 2009. D129 doi: 10.1093/nar/gkn806

[5] Han,K. and Byun,Y. (2003) Nucleic Acids Res., 31, 3432.3440.

[6] Benson, D.A. et al. (2008) Nucleic Acids Research, 36, Database Issue D25-D30.

[7] Taufer, M. et al. (2008) Parallel Computing. Volume 34, Pages: 661-680