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DNA is a chemical, and therefore, its interactions are governed by its shape. There is no way to look at a DNA sequence and know all the ramifications that changing a letter will have on its shape. I could tell you that changing the first two or last two letters of an intron are highly likely to destroy a splice site, but you can't make hard and fast ...


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This isn't a question with a really well accepted answer yet, and comes up quite a lot in e.g. studies of population variation in transcription factor motifs. Usually, we approximate the sequence preferences of a DNA-binding protein with a position weight matrix. A weight matrix will given you a score for two sequences, so the simplest means of quantifying ...



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