Fast Top-k Similar Sequence Search on DNA Databases

Top-k similar sequence search is an essential tool for DNA data management. Given a DNA database, it is a problem to extract k similar DNA sequence pairs in the database, which yield the highest similarity among all possible pairs. Although this is a fundamental problem used in the bioinformatics fi...

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Bibliographic Details
Published inInformation Integration and Web Intelligence pp. 145 - 150
Main Authors Yagi, Ryuichi, Shiokawa, Hiroaki
Format Book Chapter
LanguageEnglish
Published Cham Springer Nature Switzerland
SeriesLecture Notes in Computer Science
Subjects
DNA database
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similarity search
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Summary:Top-k similar sequence search is an essential tool for DNA data management. Given a DNA database, it is a problem to extract k similar DNA sequence pairs in the database, which yield the highest similarity among all possible pairs. Although this is a fundamental problem used in the bioinformatics field, it suffers from an expensive computational cost. To overcome these limitations, we propose a novel fast top-k similarity search algorithm for DNA databases. We conducted experiments using real-world DNA sequence datasets, and experimentally confirmed that the proposed method achieves a faster top-k search than baseline algorithms while keeping high accuracy.
ISBN:9783031210464
3031210468
ISSN:0302-9743
1611-3349
DOI:10.1007/978-3-031-21047-1_14