Multiple alignment-free sequence comparison

Jie Ren, Kai Song, Fengzhu Sun, Minghua Deng, Gesine Reinert

Abstract: Recently, a range of new statistics have become available for the alignment-free comparison of two sequences based on k-tuple word content. Here, we extend these statistics to the simultaneous comparison of more than two sequences. Our suite of statistics contains, first, and ⁠, extensions of statistics for pairwise comparison of the joint k-tuple content of all the sequences, and second, ⁠, and ⁠, averages of sums of pairwise comparison statistics. The two tasks we consider are, first, to identify sequences that are similar to a set of target sequences, and, second, to measure the similarity within a set of sequences.