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OJB©
Online Journal of Bioinformatics©
Volume 6
(2):149-161, 2005.
Binding of fork head
protein to DNA partly determined by base cooperation.
Mach V.
Institute of
Entomology, Czech Academy of Sciences, České Budějovice, Czech Republic.
ABSTRACT
Mach V,
Binding of fork head protein to DNA partly determined by base cooperation. Onl J Bioinform.,
6 (2):149-161,
2005. DNA recognition by the insect Fork
head transcription factors depends on specific combinations of neighboring
bases (base cooperation effect). This study presents a simple algorithm
designed for in silico
investigation of the effect. The algorithm measures and evaluates observed and
expected frequencies of various base combinations within the set of aligned
binding sites. Consequently, statistically significant differences between the
observed and expected frequencies are interpreted as evidence of either
positive or negative base cooperation effect. Our current results suggest that
the base cooperation affects DNA binding of the vertebrate members of the Fork
head family, similarly to their insect homologs.
Key words:
base cooperation, non-independence of bases, nucleotide combinations, DNA
binding, Fork head