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.