6533b85dfe1ef96bd12be777
RESEARCH PRODUCT
Linear-time sequence comparison using minimal absent words & applications
Robert MercaşGabriele FiciMax CrochemoreSolon P. Pississubject
0301 basic medicineLatin AmericansComputer Science (all)Library science0102 computer and information sciencesCircular wordAlgorithms on string01 natural sciencesAlignmentfree comparisonSequence comparisonTheoretical Computer Science03 medical and health sciences030104 developmental biology010201 computation theory & mathematicsInformaticsPolitical scienceAbsent wordForbidden worddescription
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realized by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free techniques, which are based on measures referring to the composition of sequences in terms of their constituent patterns. These measures, such as q-gram distance, are usually computed in time linear with respect to the length of the sequences. In this article, we focus on the complementary idea: how two sequences can be efficiently compared based on information that does not occur in the sequences. A word is an absent word of some sequence if it does not occur in the sequence. An absent word is minimal if all its proper factors occur in the sequence. Here we present the first linear-time and linear-space algorithm to compare two sequences by considering all their minimal absent words. In the process,we present results of combinatorial interest, and also extend the proposed techniques to compare circular sequences.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2016-01-01 |