hi i'm looking for a tool or online tools that creates predictions of secondary structure .i have three different sequence DNA and i checking form of these . is there site or tools for predict DNA formation example this sequence produce Z DNA or A,B i want checking interaction protein and DNA but before start my work ,i need to determine form and structure DNA
It is crucial to realize that the form of DNA is dynamic. You should not think of it as something static; I am not aware of there being any regions in the genome that are permanently in A- or Z-form.
To my understanding, conversion of DNA from the default B-form to A-form primarily happens as a response to dehydration, presumably to protect the DNA. I am thus not sure that A-form is really something you need to worry about; if you are looking for protein-DNA interactions in happily growing cells, I think you can safely ignore A-DNA.
Because Z-DNA forms a left-hand helix (as opposed to the right-hand A- and B-DNA), the formation of Z-DNA happens in response to negative supercoiling. Some work was done long ago on predicting the propensity of different DNA sequences to form Z-DNA when negatively supercoiled (Ho et al., 1986). I am not aware of a tool that you can download, though.
However, I think it is fairly safe to assume that most DNA is in B-form most of the time. If the protein you are interested binds to B-form DNA, I think you are on bit of a wild goose chase here.
This database predicts non-B DNA structures
But be careful. Lars Juhl Jensen is absolutely right, you need to be very careful in interpreting a prediction