Circular sequence comparison with q-grams

Roberto Grossi, Costas S. Iliopoulos, Robert Mercaş, Nadia Pisanti, Solon P. Pissis*, Ahmad Retha, Fatima Vayani

*Corresponding author for this work

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Abstract

Sequence comparison is a fundamental step in many important tasks in bioinformatics. Traditional algorithms for measuring approximation in sequence comparison are based on the notions of distance or similarity, and are generally computed through sequence alignment techniques. As circular genome structure is a common phenomenon in nature, a caveat of specialized alignment techniques for circular sequence comparison is that they are computationally expensive, requiring from superquadratic to cubic time in the length of the sequences. In this paper, we introduce a new distance measure based on q-grams, and show how it can be computed efficiently for circular sequence comparison. Experimental results, using real and synthetic data, demonstrate orders-of-magnitude superiority of our approach in terms of efficiency, while maintaining an accuracy very competitive to the state of the art.

Original languageEnglish
Title of host publicationAlgorithms in Bioinformatics - 15th International Workshop, WABI 2015, Proceedings
EditorsMihai Pop, Hélène Touzet
PublisherSpringer Verlag
Pages203-216
Number of pages14
ISBN (Print)9783662482209
DOIs
Publication statusPublished - 1 Jan 2015
Externally publishedYes
Event15th International Workshop on Algorithms in Bioinformatics, WABI 2015 - Atlanta, United States
Duration: 10 Sep 201512 Sep 2015

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9289
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference15th International Workshop on Algorithms in Bioinformatics, WABI 2015
Country/TerritoryUnited States
CityAtlanta
Period10/09/1512/09/15

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