title: Oligonucleotide frequency matrices addressed to recognizing functional DNA sites.
abstract: BACKGROUND
  Recognition of functional sites remains a key event in the course of genomic DNA annotation. It is well known that a number of sites have their own specific oligonucleotide content. This pinpoints the fact that the preference of the site-specific nucleotide combinations at adjacent positions within an analyzed functional site could be informative for this site recognition. Hence, Web-available resources describing the site-specific oligonucleotide content of the functional DNA sites and applying the above approach for site recognition are needed. However, they have been poorly developed up to now.
  
  
  RESULTS
  To describe the specific oligonucleotide content of the functional DNA sites, we introduce the oligonucleotide alphabets, out of which the frequency matrix for a given site could be constructed in addition to a traditional nucleotide frequency matrix. Thus, site recognition accuracy increases. This approach was implemented in the activated MATRIX database accumulating oligonucleotide frequency matrices of the functional DNA sites. We have demonstrated that the false-positive error of the functional site recognition decreases if the oligonucleotide frequency matrixes are added to the nucleotide frequency matrixes commonly used.
  
  
  BACKGROUND
  The MATRIX database is available on the Web, http://wwwmgs.bionet.nsc.ru/Dbases/MATRIX/ and the mirror site, http://www.cbil.upenn.edu/mgs/systems/c onsfreq/.
authors.affiliation: Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyeva Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru
authors.forename: M P
authors.initials: MP
authors.lastname: Ponomarenko
authors.forename: J V
authors.initials: JV
authors.lastname: Ponomarenko
authors.forename: A S
authors.initials: AS
authors.lastname: Frolov
authors.forename: O A
authors.initials: OA
authors.lastname: Podkolodnaya
authors.forename: D G
authors.initials: DG
authors.lastname: Vorobyev
authors.forename: N A
authors.initials: NA
authors.lastname: Kolchanov
authors.forename: G C
authors.initials: GC
authors.lastname: Overton
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D004247:DNA / Q000235:genetics* / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism; D016208:Databases, Factual; D016678:Genome; D008969:Molecular Sequence Data; D051839:NFI Transcription Factors; D009838:Oligodeoxyribonucleotides / Q000235:genetics; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D051839:NFI Transcription Factors; D009838:Oligodeoxyribonucleotides; D014157:Transcription Factors; C080333:transcription factor nuclear factor 1; D004247:DNA