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On-line String Matching in Highly Similar DNA Sequences

On-line String Matching in Highly Similar DNA Sequences We consider the problem of on-line exact string matching of a pattern in a set of highly similar sequences. This can be useful in cases where indexing the sequences is not feasible. We present a preliminary study by restricting the problem for a specific case where we adapt the classical Morris-Pratt and Knuth-Morris-Pratt algorithms to consider borders with errors. We give an original algorithm for computing borders at Hamming distance 1. We exhibit experimental results showing that our algorithms are much faster than searching for the pattern in each sequences with a very fast on-line exact string matching algorithm. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Mathematics in Computer Science Springer Journals

On-line String Matching in Highly Similar DNA Sequences

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References (21)

Publisher
Springer Journals
Copyright
Copyright © 2017 by Springer International Publishing
Subject
Mathematics; Mathematics, general; Computer Science, general
ISSN
1661-8270
eISSN
1661-8289
DOI
10.1007/s11786-016-0280-2
Publisher site
See Article on Publisher Site

Abstract

We consider the problem of on-line exact string matching of a pattern in a set of highly similar sequences. This can be useful in cases where indexing the sequences is not feasible. We present a preliminary study by restricting the problem for a specific case where we adapt the classical Morris-Pratt and Knuth-Morris-Pratt algorithms to consider borders with errors. We give an original algorithm for computing borders at Hamming distance 1. We exhibit experimental results showing that our algorithms are much faster than searching for the pattern in each sequences with a very fast on-line exact string matching algorithm.

Journal

Mathematics in Computer ScienceSpringer Journals

Published: Feb 2, 2017

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