Linear-time computation of prefix table for weighted strings

Carl Barton, Solon P. Pissis*

*Corresponding author for this work

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

Abstract

The prefix table of a string is one of the most fundamental data structures of algorithms on strings: it determines the longest factor at each position of the string that matches a prefix of the string. It can be computed in time linear with respect to the size of the string, and hence it can be used efficiently for locating patterns or for regularity searching in strings. A weighted string is a string in which a set of letters may occur at each position with respective occurrence probabilities. Weighted strings, also known as position weight matrices, naturally arise in many biological contexts; for example, they provide a method to realise approximation among occurrences of the same DNA segment. In this article, given a weighted string x of length n and a constant cumulative weight threshold 1/z, defined as the minimal probability of occurrence of factors in x, we present an ⱷ(n)-time algorithm for computing the prefix table of x.

Original languageEnglish
Title of host publicationCombinatorics on Words - 10th International Conference, WORDS 2015, Proceedings
EditorsDirk Nowotka, Florin Manea
PublisherSpringer Verlag
Pages73-84
Number of pages12
ISBN (Print)9783319236599
DOIs
Publication statusPublished - 1 Jan 2015
Externally publishedYes
Event10th International Conference on Words, WORDS 2015 - Kiel, Germany
Duration: 14 Sep 201517 Sep 2015

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9304
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference10th International Conference on Words, WORDS 2015
Country/TerritoryGermany
CityKiel
Period14/09/1517/09/15

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