Go to the abstract in the NAR 2001 Database Issue.
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http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html
Batenburg,F.H.D.van1, Gultyaev,A.P.1, Pleij,C.W.A.2
1Group Theoretical Biology and Phylogenetics, Inistitute of Evolutionary and Ecological Sciences, Leiden University
2Leiden Institute of Chemistry, Leiden University
Contact Batenburg@rulsfb.leidenuniv.nl
PseudoBase is a database containing structural, functional and sequence data related to RNA pseudoknots. It can be reached by its central page at http://wwwbio.LeidenUniv.nl/~Batenburg/PKB.html. 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 (like 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.
In 2001 more than 80 pseudoknot entries have been added to the database. At the time of writing the database contains 230 entries with classical H-type pseudoknots as well as more complicated ones.
Batenburg,F.H.D.van Gultyaev,A.P. and Pleij,C.W.A. (2001) PseudoBase: structural information on RNA Pseudoknots. Nucleic Acids Res., 29(1), 194-195.
Batenburg,F.H.D.van 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.
Category RNA Sequences
Go to the abstract in the NAR 2001 Database Issue.