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Online Journal of Bioinformatics©
Volume 6 (2):149-161, 2005.
Binding of fork head protein to DNA partly determined by base cooperation.
Institute of Entomology, Czech Academy of Sciences, České Budějovice, Czech Republic.
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