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Program Systems: Theory and Applications, 2014, Volume 5, Issue 4, Pages 257–267 (Mi ps139)  

This article is cited in 3 scientific papers (total in 3 papers)

Mathematical Foundations of Programming

Modeling of the optimal sequence alignment problem

Sergej Znamenskij

Program Systems Institute of RAS

Abstract: The sequence alignment is widely used in various computer systems for data similarity measure and analysis, changes detection and relative tasks. Some intuitive requirements for string alignment are formalised in a test suite. The tests shows that none of existing approaches to string similarities and alignment meet the requirements. A new model of minimizing conflicts when merging changes is described. The model leads to a simple formulation of new optimization problem which meet the requirements. (In Russian).

Key words and phrases: similarity of strings, sequence alignment, edit distance, diff, LCS, Levenshtein metric, software development, continuous integration.

Full text: PDF file (1079 kB)
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UDC: 004.416
Received: 14.12.2014
Accepted: 31.12.2014

Citation: Sergej Znamenskij, “Modeling of the optimal sequence alignment problem”, Program Systems: Theory and Applications, 5:4 (2014), 257–267

Citation in format AMSBIB
\Bibitem{Zna14}
\by Sergej~Znamenskij
\paper Modeling of the optimal sequence alignment problem
\jour Program Systems: Theory and Applications
\yr 2014
\vol 5
\issue 4
\pages 257--267
\mathnet{http://mi.mathnet.ru/ps139}


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  • http://mi.mathnet.ru/eng/ps139
  • http://mi.mathnet.ru/eng/ps/v5/i4/p257

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    Citing articles on Google Scholar: Russian citations, English citations
    Related articles on Google Scholar: Russian articles, English articles

    This publication is cited in the following articles:
    1. V. A. Roganov, A. A. Kuznetsov, G. A. Matveev, V. I. Osipov, “Metody adaptatsii sistemy parallelnogo programmirovaniya OpenTS dlya podderzhki raboty T-prilozhenii na gibridnykh vychislitelnykh klasterakh”, Programmnye sistemy: teoriya i prilozheniya, 4:4 (2013), 17–31  mathnet
    2. Sergej V. Znamenskij, “Simple essential improvements to the ROUGE-W algorithm”, Zhurn. SFU. Ser. Matem. i fiz., 8:4 (2015), 497–501  mathnet  crossref
    3. S. V. Znamenskij, “A model and algorithm for sequence alignment”, Programmnye sistemy: teoriya i prilozheniya, 6:1 (2015), 189–197  mathnet
  • Program Systems: Theory and Applications
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