When I get results back, in the transcription factor binding sites, sometimes sequences were colored with blue and red. I wonder what this color means?
Submitted: 2004/03/18; Answered: 2004/03/18 by Jonathan Schug For the log-likelihood score, each position of the weight matrix has a best possible score for that position. If a letter is black, then the score it got is within 0.1 of the best possible score for that position. For example, if the position corresponds to an S (C or G) then we don’t (visually) indicate an occurrence of the second-most frequently observed (or any other alternative) base if it is nearly (within 0.1 bit) as good as the most frequent. Blue is used when the score for a base is within 1 bit of the best possible score. This is indicates a mismatch, but not one that is very bad. Mismatches that are worse are colored red.
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