Sequence similarity measures based on bounded hamming distance

Alberto Apostolico; Concettina Guerra; Gad M. Landau; Cinzia Pizzi

doi:10.1016/j.tcs.2016.01.023

Sequence similarity measures based on bounded hamming distance

Alberto Apostolico, Concettina Guerra, Gad M. Landau, Cinzia Pizzi

Department of Computer Science

Research output: Contribution to journal › Article › peer-review

Abstract

A growing number of measures of sequence similarity are being based on some underlying notion of relative compressibility. Within this paradigm, similar sequences are expected to share a large number of common substrings, or subsequences, or more complex patterns or motifs, and so on. In this paper, measures of sequence similarity are introduced and studied in which patterns in a pair are considered similar if they coincide up to a preset number of mismatches, that is, within a bounded Hamming distance. It is shown here that for some such measures bounds are achievable that are slightly better than O(n²). Preliminary experiments demonstrate the potential applicability to phylogeny and classification of these similarity measures.

Original language	English
Pages (from-to)	76-90
Number of pages	15
Journal	Theoretical Computer Science
Volume	638
DOIs	https://doi.org/10.1016/j.tcs.2016.01.023
State	Published - 25 Jul 2016

Bibliographical note

Funding Information:
A. Apostolico was supported in part by United States–Israel Binational Science Foundation (BSF) Grants Nos. 2008217 and 2014028 . C. Guerra was supported in part by United States–Israel Binational Science Foundation (BSF) Grant No. 2014028 . G. Landau was partially supported by the National Science Foundation Award 0904246 , Israel Science Foundation grants 347/09 and 571/14 , Grants Nos. 2008217 and 2014028 from the United States–Israel Binational Science Foundation (BSF) and DFG . C. Pizzi was partially supported by PRIN No. 20122F87B2 , financed by the Italian MIUR .

Publisher Copyright:
© 2016 Elsevier B.V.

Keywords

Alignment free distances
Binary string
Longest common substring
Mismatches
Pattern matching
String comparison

ASJC Scopus subject areas

Theoretical Computer Science
Computer Science (all)

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10.1016/j.tcs.2016.01.023

Cite this

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abstract = "A growing number of measures of sequence similarity are being based on some underlying notion of relative compressibility. Within this paradigm, similar sequences are expected to share a large number of common substrings, or subsequences, or more complex patterns or motifs, and so on. In this paper, measures of sequence similarity are introduced and studied in which patterns in a pair are considered similar if they coincide up to a preset number of mismatches, that is, within a bounded Hamming distance. It is shown here that for some such measures bounds are achievable that are slightly better than O(n2). Preliminary experiments demonstrate the potential applicability to phylogeny and classification of these similarity measures.",

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AU - Guerra, Concettina

AU - Landau, Gad M.

AU - Pizzi, Cinzia

N1 - Funding Information: A. Apostolico was supported in part by United States–Israel Binational Science Foundation (BSF) Grants Nos. 2008217 and 2014028 . C. Guerra was supported in part by United States–Israel Binational Science Foundation (BSF) Grant No. 2014028 . G. Landau was partially supported by the National Science Foundation Award 0904246 , Israel Science Foundation grants 347/09 and 571/14 , Grants Nos. 2008217 and 2014028 from the United States–Israel Binational Science Foundation (BSF) and DFG . C. Pizzi was partially supported by PRIN No. 20122F87B2 , financed by the Italian MIUR . Publisher Copyright: © 2016 Elsevier B.V.

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N2 - A growing number of measures of sequence similarity are being based on some underlying notion of relative compressibility. Within this paradigm, similar sequences are expected to share a large number of common substrings, or subsequences, or more complex patterns or motifs, and so on. In this paper, measures of sequence similarity are introduced and studied in which patterns in a pair are considered similar if they coincide up to a preset number of mismatches, that is, within a bounded Hamming distance. It is shown here that for some such measures bounds are achievable that are slightly better than O(n2). Preliminary experiments demonstrate the potential applicability to phylogeny and classification of these similarity measures.

AB - A growing number of measures of sequence similarity are being based on some underlying notion of relative compressibility. Within this paradigm, similar sequences are expected to share a large number of common substrings, or subsequences, or more complex patterns or motifs, and so on. In this paper, measures of sequence similarity are introduced and studied in which patterns in a pair are considered similar if they coincide up to a preset number of mismatches, that is, within a bounded Hamming distance. It is shown here that for some such measures bounds are achievable that are slightly better than O(n2). Preliminary experiments demonstrate the potential applicability to phylogeny and classification of these similarity measures.

KW - Alignment free distances

KW - Binary string

KW - Longest common substring

KW - Mismatches

KW - Pattern matching

KW - String comparison

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JO - Theoretical Computer Science

JF - Theoretical Computer Science

ER -

Sequence similarity measures based on bounded hamming distance

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

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