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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
ABSTRACT
Mach V, Binding of fork head protein to DNA
partly determined by base cooperation. Online J
Bioinformatics, 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