The SCP and Compressed Domain Analysis of Biological Sequences
نویسندگان
چکیده
We introduce the SCP the sorted common prefix, and study some of its properties. Based on the internal representations used by a class of new compression schemes, we show how the SCP table can be constructed using an ( ) max κ Σ + u O number of comparisons on average, and ( ) Σ u O worst case, where u is the size of the sequence, Σ is the number of symbols, and max κ is the maximum SCP value. We describe how two applications of the SCP in biological sequence analysis. In particular, using the SCP, and the compressed representation of the sequence, we present an algorithm for finding all the occ η canonical tandem arrays in the sequence in ( ) max κ η Σ + + occ u O time on average, and ( ) Σ + u O occ η worst case. Preliminary results on the statistics of the SCP for some DNA and protein sequences are included.
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