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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Bibliographic Details
Published in:International Conference in Information, Communication and Automation Technologies (Online) pp. 1 - 6
Main Authors: Terzic, Dzenana, Pita, Naida, Becirspahic, Nejla, Muhic, Dzenis
Format: Conference Proceeding
Language:English
Published: IEEE 02.09.2025
Subjects:
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 Access:Get full text
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Summary: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.
ISSN:2643-1858
DOI:10.1109/ICAT66432.2025.11189285