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Nucleic Acids Research, 2001, Vol. 29, No. 1 312-316
© 2001 Oxford University Press

rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations

Julia V. Ponomarenko*, Tatyana I. Merkulova, Gennady V. Vasiliev, Zoya B. Levashova, Galina V. Orlova, Sergey V. Lavryushev, Oleg N. Fokin, Mikhail P. Ponomarenko, Anatoly S. Frolov and Akinori Sarai1

Institute of Cytology and Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia and 1The Institute of Physical and Chemical Research, RIKEN, 3-1-1 Koyadai, Tsukuba, Japan

rSNP_Guide is a novel curated database system for analysis of transcription factor (TF) binding to target sequences in regulatory gene regions altered by mutations. It accumulates experimental data on naturally occurring site variants in regulatory gene regions and site-directed mutations. This database system also contains the web tools for SNP analysis, i.e., active applet applying weight matrices to predict the regulatory site candidates altered by a mutation. The current version of the rSNP_Guide is supplemented by six sub-databases: (i) rSNP_DB, on DNA–protein interaction caused by mutation; (ii) SYSTEM, on experimental systems; (iii) rSNP_BIB, on citations to original publications; (iv) SAMPLES, on experimentally identified sequences of known regulatory sites; (v) MATRIX, on weight matrices of known TF sites; (vi) rSNP_Report, on characteristic examples of successful rSNP_Tools implementation. These databases are useful for the analysis of natural SNPs and site-directed mutations. The databases are available through the Web, http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/.

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


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