Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (94K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (20)
Right arrowRequest Permissions
Citing Articles
Right arrowScopus Links
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by van Batenburg, F. H. D.
Right arrow Articles by Pleij, C. W. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by van Batenburg, F. H. D.
Right arrow Articles by Pleij, C. W. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2001, Vol. 29, No. 1 194-195
© 2001 Oxford University Press

PseudoBase: structural information on RNA pseudoknots

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

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.LeidenUniv.nl/~Batenburg/PKB.html. For each pseudoknot, thirteen items are stored, for example the relevant sequence, the stem positions of the pseudoknot, the EMBL accession number of the sequence and the support that can be given regarding the reliability of the pseudo­knot. Since the last publication, information on sizes of the stems and the loops in the pseudoknots has been added. Also added are alternative entries that produce surveys of where the pseudoknots are, sorted according to stem size or loop size.

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


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
I. Dotu, W. A. Lorenz, P. Van Hentenryck, and P. Clote
Computing folding pathways between RNA secondary structures
Nucleic Acids Res., March 1, 2010; 38(5): 1711 - 1722.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
M. S. Andronescu, C. Pop, and A. E. Condon
Improved free energy parameters for RNA pseudoknotted secondary structure prediction
RNA, January 1, 2010; 16(1): 26 - 42.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
Y. Byun and K. Han
PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots
Bioinformatics, June 1, 2009; 25(11): 1435 - 1437.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. P. Gardner, J. Daub, J. G. Tate, E. P. Nawrocki, D. L. Kolbe, S. Lindgreen, A. C. Wilkinson, R. D. Finn, S. Griffiths-Jones, S. R. Eddy, et al.
Rfam: updates to the RNA families database
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D136 - D140.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. Theis, J. Reeder, and R. Giegerich
KnotInFrame: prediction of -1 ribosomal frameshift events
Nucleic Acids Res., October 1, 2008; 36(18): 6013 - 6020.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
S. Pennell, E. Manktelow, A. Flatt, G. Kelly, S. J. Smerdon, and I. Brierley
The stimulatory RNA of the Visna-Maedi retrovirus ribosomal frameshifting signal is an unusual pseudoknot with an interstem element
RNA, July 1, 2008; 14(7): 1366 - 1377.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Byun and K. Han
PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W416 - W422.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
J. REN, B. RASTEGARI, A. CONDON, and H. H. HOOS
HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots
RNA, October 1, 2005; 11(10): 1494 - 1504.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
C.-H. Huang, C. L. Lu, and H.-T. Chiu
A heuristic approach for detecting RNA H-type pseudoknots
Bioinformatics, September 1, 2005; 21(17): 3501 - 3508.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Han and Y. Byun
PSEUDOVIEWER2: visualization of RNA pseudoknots of any type
Nucleic Acids Res., July 1, 2003; 31(13): 3432 - 3440.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Griffiths-Jones, A. Bateman, M. Marshall, A. Khanna, and S. R. Eddy
Rfam: an RNA family database
Nucleic Acids Res., January 1, 2003; 31(1): 439 - 441.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
P. Schattner
Searching for RNA genes using base-composition statistics
Nucleic Acids Res., May 1, 2002; 30(9): 2076 - 2082.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.