Multiple alignment-free sequence comparison.

ABSTRACT:

Motivation

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, C(*)1 and C(S)1, extensions of statistics for pairwise comparison of the joint k-tuple content of all the sequences, and second, C(*)2, C(S)2 and C(geo)2, 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.

Results

Our investigation uses both simulated data as well as cis-regulatory module data where the task is to identify ci

SUBMITTER: Ren J 

PROVIDER: S-EPMC3799466 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature