Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (152K) 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 (6)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Ponomarenko, J. V.
Right arrow Articles by Ponomarenko, M. P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Ponomarenko, J. V.
Right arrow Articles by Ponomarenko, M. P.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2002, Vol. 30, No. 1 195-199
© 2002 Oxford University Press

SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data

Julia V. Ponomarenko*, Galina V. Orlova, Anatoly S. Frolov, Mikhail S. Gelfand1 and Mikhail P. Ponomarenko

Institute of Cytology and Genetics, 10 Lavrentyev Avenue, Novosibirsk 630090, Russia and 1Integrated Genomics, Moscow Branch, PO Box 348, Moscow 117333, Russia

SELEX_DB is an online resource containing both the experimental data on in vitro selected DNA/RNA oligomers (aptamers) and the applets for recognition of these oligomers. Since in vitro experimental data are evidently system-dependent, the new release of the SELEX_DB has been supplemented by the database SYSTEM storing the experimental design. In addition, the recognition applet package, SELEX_TOOLS, applying in vitro selected data to annotation of the genome DNA, is accompanied by the cross-validation test database CROSS_TEST discriminating the sites (natural or other) related to in vitro selected sites out of random DNA. By cross-validation testing, we have unexpectedly observed that the recognition accuracy increases with the growth of homology between the training and test sets of protein binding sequences. For natural sites, the recognition accuracy was lower than that for the nearest protein homologs and higher than that for distant homologs and non-homologous proteins binding the common site. The current SELEX_DB release is available at http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/.

* To whom correspondence should be addressed. Tel: +7 383 2 333 119; Fax: +7 383 2 331 278; Email: jpon{at}bionet.nsc.ru


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
J. F. Lee, J. R. Hesselberth, L. A. Meyers, and A. D. Ellington
Aptamer Database
Nucleic Acids Res., January 1, 2004; 32(90001): D95 - 100.
[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.