The binding of fork head proteins to DNA is partly determined by cooperation of bases
| Autor: | Václav Mach |
|---|---|
| Rok vydání: | 2006 |
| Předmět: |
Genetics
genetic structures General Immunology and Microbiology QH301-705.5 Head (linguistics) General Neuroscience In silico dna binding base cooperation Biology non-independence of bases Base (topology) General Biochemistry Genetics and Molecular Biology Fork (software development) chemistry.chemical_compound Negative base chemistry Evolutionary biology Biology (General) Binding site General Agricultural and Biological Sciences Transcription factor nucleotide combinations DNA fork head |
| Zdroj: | Open Life Sciences, Vol 1, Iss 4, Pp 594-608 (2006) |
| ISSN: | 2391-5412 |
| DOI: | 10.2478/s11535-006-0036-0 |
| Popis: | Our previous study revealed that DNA recognition by the insect Fork head transcription factors depends on specific combinations of neighboring bases, a phenomenon called the base cooperation effect. This study presents a simple algorithm designed for in silico investigation of the base cooperation effect. The algorithm measures and evaluates observed and expected frequencies of various base combinations within a 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 homologies. The statistical algorithm used in this study is available on line (http://blast.entu.cas.cz/bias/index.htm). |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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