RelativeFreq takes the words found in a given target sequence and calculates the relative frequency of those words in two different source sequences (source 1 and source 2), which may be of different sizes. RelativeFreq analyses have four steps. First, all words of length k present in the target sequence are searched for in each of the two source sequences using a routine identical to that in OligoProfile. Second, the program establishes the relative frequencies of those words in the two source sequences, dividing the frequency in source 1 by the frequency in source 2. To avoid errors, all zero frequency values in source 2 are conservatively substituted by frequency = 0.5. Third, the program corrects the relative frequencies found, taking into account the sizes of both source sequences. Finally, the program generates a smoothed representation of the relative frequencies, similar to the one obtained with Smoothing, by averaging the frequency of R contiguous values.
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This analysis can take a few seconds
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