Parallel DNA Sequencing using Exact String-Matching Algorithms for Multiple Patterns

String matching algorithms are used to find specific patterns within a larger file or sequence. They are extensively used in bioinformatics, molecular biology, and information retrieval. With the world of data at our fingertips, the aim is to accelerate its processing. This study focuses on applying...

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Veröffentlicht in:International Conference in Information, Communication and Automation Technologies (Online) S. 1 - 6
Hauptverfasser: Terzic, Dzenana, Pita, Naida, Becirspahic, Nejla, Muhic, Dzenis
Format: Tagungsbericht
Sprache:Englisch
Veröffentlicht: IEEE 02.09.2025
Schlagworte:
Bioinformatics
Brute Force
Burrows-Wheeler transform
CUDA
DNA
exact
FM Index
Force
Frequency modulation
Indexes
parallel
Pattern matching
Sequential analysis
Sorting
String-matching
Suffix Array
Testing
Time complexity
Transforms
ISSN:2643-1858
Online-Zugang:Volltext
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Abstract String matching algorithms are used to find specific patterns within a larger file or sequence. They are extensively used in bioinformatics, molecular biology, and information retrieval. With the world of data at our fingertips, the aim is to accelerate its processing. This study focuses on applying two distinctive parallel approaches to multiple substring matching in DNA. A Brute Force and FM Index algorithm are implemented, and their strengths and weaknesses are discussed based on experiments conducted on real genome sequences.
AbstractList String matching algorithms are used to find specific patterns within a larger file or sequence. They are extensively used in bioinformatics, molecular biology, and information retrieval. With the world of data at our fingertips, the aim is to accelerate its processing. This study focuses on applying two distinctive parallel approaches to multiple substring matching in DNA. A Brute Force and FM Index algorithm are implemented, and their strengths and weaknesses are discussed based on experiments conducted on real genome sequences.
Author Pita, Naida
Terzic, Dzenana
Muhic, Dzenis
Becirspahic, Nejla
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  surname: Becirspahic
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  surname: Muhic
  fullname: Muhic, Dzenis
  email: dmuhic1@etf.unsa.ba
  organization: Faculty of Electrical Engineering,Department of Computing and Informatics,Sarajevo,Bosnia and Herzegovina
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Snippet String matching algorithms are used to find specific patterns within a larger file or sequence. They are extensively used in bioinformatics, molecular biology,...
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SubjectTerms Bioinformatics
Brute Force
Burrows-Wheeler transform
CUDA
DNA
exact
FM Index
Force
Frequency modulation
Indexes
parallel
Pattern matching
Sequential analysis
Sorting
String-matching
Suffix Array
Testing
Time complexity
Transforms
Title Parallel DNA Sequencing using Exact String-Matching Algorithms for Multiple Patterns
URI https://ieeexplore.ieee.org/document/11189285
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