Naslov
Estimating Mutation Distances from Unaligned Genomes

Autori
Haubold, Bernhard ; Pfaffelhuber, Peter ; Domazet-Lošo, Mirjana ; Wiehe, Thomas

Izvornik
Journal of Computational Biology (1066-5277) 16 (2009), 10; 1487-1500

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
alignment-free distance; number of substitutions; genome comparison; suffix tree; shortest unique substring

Sažetak
Alignment-free distance measures are generally less accurate but more efficient than traditional alignment-based metrics. In the context of genome sequence analysis, the efficiency gain is often so substantial that it outweights the loss in accuracy. However, a further disadvantage of alignment-free distances is that their relationship to evolutionary events such as substitutions is generally unknown. We have therefore derived an estimator of the number of substitutions per site between two unaligned DNA sequences, Kr. Simulations show that this estimator works well with ‘ ‘ ideal’ ’ data. We compare Kr to two alternative alignment-free distances: a k-tuple distance and a measure of relative entropy based on average common substring length. All three measures are applied to 27 primate mitochondrial genomes, eight whole genomes of Streptococcus agalactiae strains, and 12 whole genomes of Drosophila species. In each case, the cluster diagrams based on Kr are equivalent to or significantly better than those based on the two alternative measures. This is due to the fact that in contrast to the alternative measures Kr is derived from an explicit model of evolution. The computation of Kr is efficiently implemented in the program kr, which can be downloaded freely from the internet.

Izvorni jezik
Engleski

Znanstvena područja
Biologija, Računarstvo

POVEZANOST RADA