Absent words and the (dis)similarity analysis of DNA sequences: An experimental study

Abstract

Background: An absent word with respect to a sequence is a word that does not occur in the sequence as a factor; an absent word is minimal if all its factors on the other hand occur in that sequence. In this paper we explore the idea of using minimal absent words (MAW) to compute the distance between two biological sequences. The motivation and rationale of our work comes from the potential advantage of being able to extract as little information as possible from large genomic sequences to reach the goal of comparing sequences in an alignment-free manner. Findings: We report an experimental study on the use of absent words as a distance measure among biological sequences. We provide recommendations to use the best index based on our analysis. In particular, our analysis reveals that the best performers are: the length weighted index of relative absent word sets, the length weighted index of the symmetric difference of the MAW sets, and the Jaccard distance between the MAW sets. We also found that during the computation of the absent words, the reverse complements of the sequences should also be considered. Conclusion: The use of MAW to compute the distance between two biological sequences has potential advantage over alignment based methods. It is expected that this potential advantage would encourage researchers and practitioners to use this as a (dis)similarity measure in the context of sequence comparison and phylogeny reconstruction. Therefore, we present here a comparison among different possible models and indexes and pave the path for the biologists and researchers to choose an appropriate model for such comparisons.