Kalign-LCS —a more accurate and faster variant of kalign2 algorithm for the multiple sequence alignment problem

Sebastian Deorowicz; Agnieszka Debudaj-Grabysz; Adam Gudyś

doi:10.1007/978-3-319-02309-0_54

Kalign-LCS —a more accurate and faster variant of kalign2 algorithm for the multiple sequence alignment problem

Sebastian Deorowicz
, Agnieszka Debudaj-Grabysz
, Adam Gudyś

Department of Algorithmics and Software (RAU/RAU5)

Silesian University of Technology

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

8 Citations (Scopus)

Abstract

Determination of similarities between species is a crucial issue in life sciences. This task is usually done by comparing fragments of genomic or proteomic sequences of organisms subjected to analysis. The basic procedure which facilitates these comparisons is called multiple sequence alignment. There are a lot of algorithms aiming at this problem, which are either accurate or fast. We present Kalign-LCS, a variant of fast Kalign2 algorithm, that addresses the accuracy vs. speed trade-off. It employs the longest common subsequencemeasure and was thoroughly optimized. Experiments show that it is faster than Kalign2 and produces noticeably more accurate alignments.

Original language	English
Title of host publication	Man-Machine Interactions 3
Editors	Aleksandra Gruca, Tadeusz Czachórski, Stanisław Kozielski, Tadeusz Czachórski
Publisher	Springer Verlag
Pages	495-502
Number of pages	8
ISBN (Electronic)	9783319023083
DOIs	https://doi.org/10.1007/978-3-319-02309-0_54
Publication status	Published - 2014
Event	3rd International Conference on Man-Machine Interactions, ICMMI 2013 - Brenna, Poland Duration: 22 Oct 2013 → 25 Oct 2013

Publication series

Name	Advances in Intelligent Systems and Computing
Volume	242
ISSN (Print)	2194-5357

Conference

Conference	3rd International Conference on Man-Machine Interactions, ICMMI 2013
Country/Territory	Poland
City	Brenna
Period	22/10/13 → 25/10/13

Keywords

Longest common subsequence
Multiple sequence alignment

ASJC Scopus subject areas

Control and Systems Engineering
General Computer Science

Access to Document

10.1007/978-3-319-02309-0_54

Cite this

Deorowicz, S., Debudaj-Grabysz, A., & Gudyś, A. (2014). Kalign-LCS —a more accurate and faster variant of kalign2 algorithm for the multiple sequence alignment problem. In A. Gruca, T. Czachórski, S. Kozielski, & T. Czachórski (Eds.), Man-Machine Interactions 3 (pp. 495-502). (Advances in Intelligent Systems and Computing; Vol. 242). Springer Verlag. https://doi.org/10.1007/978-3-319-02309-0_54

Deorowicz, Sebastian ; Debudaj-Grabysz, Agnieszka ; Gudyś, Adam. / Kalign-LCS —a more accurate and faster variant of kalign2 algorithm for the multiple sequence alignment problem. Man-Machine Interactions 3. editor / Aleksandra Gruca ; Tadeusz Czachórski ; Stanisław Kozielski ; Tadeusz Czachórski. Springer Verlag, 2014. pp. 495-502 (Advances in Intelligent Systems and Computing).

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title = "Kalign-LCS {\textemdash}a more accurate and faster variant of kalign2 algorithm for the multiple sequence alignment problem",

abstract = "Determination of similarities between species is a crucial issue in life sciences. This task is usually done by comparing fragments of genomic or proteomic sequences of organisms subjected to analysis. The basic procedure which facilitates these comparisons is called multiple sequence alignment. There are a lot of algorithms aiming at this problem, which are either accurate or fast. We present Kalign-LCS, a variant of fast Kalign2 algorithm, that addresses the accuracy vs. speed trade-off. It employs the longest common subsequencemeasure and was thoroughly optimized. Experiments show that it is faster than Kalign2 and produces noticeably more accurate alignments.",

keywords = "Longest common subsequence, Multiple sequence alignment",

author = "Sebastian Deorowicz and Agnieszka Debudaj-Grabysz and Adam Gudy{\'s}",

note = "Publisher Copyright: {\textcopyright} Springer India 2014.; 3rd International Conference on Man-Machine Interactions, ICMMI 2013 ; Conference date: 22-10-2013 Through 25-10-2013",

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doi = "10.1007/978-3-319-02309-0\_54",

language = "English",

series = "Advances in Intelligent Systems and Computing",

publisher = "Springer Verlag",

pages = "495--502",

editor = "Aleksandra Gruca and Tadeusz Czach{\'o}rski and Stanis{\l}aw Kozielski and Tadeusz Czach{\'o}rski",

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Deorowicz, S, Debudaj-Grabysz, A & Gudyś, A 2014, Kalign-LCS —a more accurate and faster variant of kalign2 algorithm for the multiple sequence alignment problem. in A Gruca, T Czachórski, S Kozielski & T Czachórski (eds), Man-Machine Interactions 3. Advances in Intelligent Systems and Computing, vol. 242, Springer Verlag, pp. 495-502, 3rd International Conference on Man-Machine Interactions, ICMMI 2013, Brenna, Poland, 22/10/13. https://doi.org/10.1007/978-3-319-02309-0_54

Kalign-LCS —a more accurate and faster variant of kalign2 algorithm for the multiple sequence alignment problem. / Deorowicz, Sebastian; Debudaj-Grabysz, Agnieszka; Gudyś, Adam.
Man-Machine Interactions 3. ed. / Aleksandra Gruca; Tadeusz Czachórski; Stanisław Kozielski; Tadeusz Czachórski. Springer Verlag, 2014. p. 495-502 (Advances in Intelligent Systems and Computing; Vol. 242).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AU - Gudyś, Adam

N1 - Publisher Copyright: © Springer India 2014.

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N2 - Determination of similarities between species is a crucial issue in life sciences. This task is usually done by comparing fragments of genomic or proteomic sequences of organisms subjected to analysis. The basic procedure which facilitates these comparisons is called multiple sequence alignment. There are a lot of algorithms aiming at this problem, which are either accurate or fast. We present Kalign-LCS, a variant of fast Kalign2 algorithm, that addresses the accuracy vs. speed trade-off. It employs the longest common subsequencemeasure and was thoroughly optimized. Experiments show that it is faster than Kalign2 and produces noticeably more accurate alignments.

AB - Determination of similarities between species is a crucial issue in life sciences. This task is usually done by comparing fragments of genomic or proteomic sequences of organisms subjected to analysis. The basic procedure which facilitates these comparisons is called multiple sequence alignment. There are a lot of algorithms aiming at this problem, which are either accurate or fast. We present Kalign-LCS, a variant of fast Kalign2 algorithm, that addresses the accuracy vs. speed trade-off. It employs the longest common subsequencemeasure and was thoroughly optimized. Experiments show that it is faster than Kalign2 and produces noticeably more accurate alignments.

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A2 - Czachórski, Tadeusz

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PB - Springer Verlag

T2 - 3rd International Conference on Man-Machine Interactions, ICMMI 2013

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ER -

Kalign-LCS —a more accurate and faster variant of kalign2 algorithm for the multiple sequence alignment problem

Abstract

Publication series

Conference

Keywords

ASJC Scopus subject areas

Access to Document

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Cite this