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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 O(u+| Σ |Kmax) number of comparisons on average, and O(u | Σ |) worst case, where u is the size of the sequence, | Σ | is the number of symbols, and Kmax is the maximum SCP value. We describe one application of the SCP to the problem of anchor points in multiple sequence alignment.
Date of Conference: 11-14 Aug. 2003