I have 10,000 fixed length strings of DNA sequences. An example would be
ATTGGGT M GCGGCTG. Now the character marked M is a position of interest to me (say something that causes diseases). Similarly, I have data for non-disease sequences also where the position of interest doesn't cause a disease.
How can I say that the neighbouring sequences like A,T,T,G,G,G,T to the left or G,C,G,G,C,T,G to the right have an influence on M being a disease-causing/non-disease causing position in the sequence.

How can I conclude something like T in the immediate left of M has more influence than A in the seventh position to the left of M.
I thought of using regression to predict M using the neighborhood sequences but I am not sure whether that would work. Can I use some clever encoding techniques to prove the above hypothesis? Any help is greatly appreciated.


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.