The Extract program was devised to be used after OligoProfile. It allows the user to obtain regions of a target sequence that are deemed interesting after considering the OligoProfile results. Once the target is uploaded or selected, this program uses four parameters, namely k, R, Start position and Number of segments to establish the DNA sequence to be extracted. The first three parameters are needed to define the starting point of the sequence to be retrieved based on OligoProfile results. For example, let us imagine an OligoProfile analysis generated with k = 13 and R = 1000 in which we find a region of the target sequence which seems particularly interesting given that it generates 5 contiguous values (e. g. values 353 to 357) with particularly low frequencies. We can obtain the DNA sequence corresponding to this region by providing the Extract program with the k and R values used in OligoProfile and with the number that corresponds to the first window of the region (Start position = 353) plus the number of consecutive regions to be retrieved (No. of segments; they indeed correspond to contiguous segments in the DNA sequence) which, in our example, would be equal to 5. The sequence extracted in this example would have a total of R times the number of segments, i. e. 5000 words.
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This analysis can take a few seconds
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