Alignment-free phylogeny of whole genomes using underlying subwords.

ABSTRACT:

Unlabelled

Background

With the progress of modern sequencing technologies a large number of complete genomes are now available. Traditionally the comparison of two related genomes is carried out by sequence alignment. There are cases where these techniques cannot be applied, for example if two genomes do not share the same set of genes, or if they are not alignable to each other due to low sequence similarity, rearrangements and inversions, or more specifically to their lengths when the organisms belong to different species. For these cases the comparison of complete genomes can be carried out only with ad hoc methods that are usually called alignment-free methods.

Methods

In this paper we propose a distance function based on subword compositions called Underlying Ap

SUBMITTER: Comin M 

PROVIDER: S-EPMC3549825 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature