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Backward Pattern Matching on Elastic Degenerate Strings

The result's identifiers

  • Result code in IS VaVaI

    <a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68407700%3A21240%2F21%3A00349682" target="_blank" >RIV/68407700:21240/21:00349682 - isvavai.cz</a>

  • Result on the web

  • DOI - Digital Object Identifier

Alternative languages

  • Result language

    angličtina

  • Original language name

    Backward Pattern Matching on Elastic Degenerate Strings

  • Original language description

    Recently, the concept of Elastic Degenerate Strings (EDS) was introduced as a way of representing a sequenced population of the same species. Several on-line Elastic Degenerate String Matching (EDSM) algorithms were presented so far. Some of them provide practical implementation. We propose a new on-line EDSM algorithm BNDM-EDS. Our algorithm combines two traditional algorithms BNDM and the Shift-And that were adapted to the specifics needed by Elastic Degenerate Strings. BNDM-EDS is running in O (Nmd m w e) worst-case time. This implies O (Nm) time for small patterns, where m is the length of the searched pattern, N is the size of EDS, and w is the size of the computer word. The algorithm uses O (N + n) space, where n is the length of EDS. BNDM-EDS requires a simple preprocessing step with time and space O (m). Experimental results on real genomic data show superiority of BNDM-EDS over state-of-the-art algorithms.

  • Czech name

  • Czech description

Classification

  • Type

    D - Article in proceedings

  • CEP classification

  • OECD FORD branch

    10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Result continuities

  • Project

    <a href="/en/project/GA19-20759S" target="_blank" >GA19-20759S: Efficient String Matching for Bioinformatics</a><br>

  • Continuities

    P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Others

  • Publication year

    2021

  • Confidentiality

    S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Data specific for result type

  • Article name in the collection

    Proceedings of 14th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2021)

  • ISBN

    978-989-758-490-9

  • ISSN

    2184-4305

  • e-ISSN

  • Number of pages

    10

  • Pages from-to

    50-59

  • Publisher name

    SCITEPRESS – Science and Technology Publications, Lda

  • Place of publication

    Lisboa

  • Event location

    Prague

  • Event date

    Feb 11, 2021

  • Type of event by nationality

    WRD - Celosvětová akce

  • UT code for WoS article

    000664105700004