Oligonucleotide frequency matrices addressed to recognizing functional DNAsites

Motivation: Recognition of functional sires remains a key evens in the cour se of genomic DNA annotation. It is well known,rn that a number of sires ha ve their own specific oligonucleotide content. This pinpoints the fact that the preference of the site-specific nucleotide combinations at adjacent po sitions within an analyzed functional sire could be informative for this si te recognition. Hence, Web-available resources describing the site-specific oligonucleotide content of the functional DNA sites and applying the above approach for sire recognition are needed. However; they have been poorly d eveloped up to now. Results: To describe the specific oligonucleotide content of the functional DNA sites, bye introduce the oligonucleotide alphabets, out of which the f requency matrix for a given site could be constructed ir? addition to a tra ditional nucleotide frequency matrix. Thus, sire recognition accuracy incre ases. This approach was implemented in the activated MATRIX database accumu lating oligonucleotide frequency matrices of the functional DNA sites. We h ave demonstrated that the false-positive error of the functional site recog nition decreases if the oligonucleotide frequency matrixes are added to the nucleotide frequency matrixes commonly used Availability: The MATRIX database is available on the Web, http://wwwmgs.bi onet.nsc.ru/Dbases/MATRIX/ and the mirror site, http://www.cbil.upenn.edu/m gs/systems/consfreq/. Contact: pon@bionet.nsc.ru.