title: SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data.
abstract: 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/.
authors.affiliation: Institute of Cytology and Genetics, 10 Lavrentyev Avenue, Novosibirsk 630090, Russia and Integrated Genomics, Moscow Branch, PO Box 348, Moscow 117333, Russia. jpon@bionet.nsc.ru
authors.forename: Julia V
authors.initials: JV
authors.lastname: Ponomarenko
authors.forename: Galina V
authors.initials: GV
authors.lastname: Orlova
authors.forename: Anatoly S
authors.initials: AS
authors.lastname: Frolov
authors.forename: Mikhail S
authors.initials: MS
authors.lastname: Gelfand
authors.forename: Mikhail P
authors.initials: MP
authors.lastname: Ponomarenko
mesh_terms: D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D003628:Database Management Systems; D030561:Databases, Nucleic Acid; D006801:Humans; D016247:Information Storage and Retrieval; D020407:Internet; D016297:Mutagenesis, Site-Directed; D009841:Oligonucleotides / Q000235:genetics* / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D017385:Sequence Homology
chemical_list: D004268:DNA-Binding Proteins; D009841:Oligonucleotides