The SCP and compressed domain analysis of biological sequences

Abstract

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+| /spl Sigma/ |K/sub max/) number of comparisons on average, and O(u | /spl Sigma/ |) worst case, where u is the size of the sequence, | /spl Sigma/ | is the number of symbols, and K/sub max/ is the maximum SCP value. We describe one application of the SCP to the problem of anchor points in multiple sequence alignment.