A Comparative study of DNA Alignment Algorithms and Boosting Performance Using Different Compilation Strategies

Osman Doluca

doi:10.17776/csj.1511642

EN TR

A Comparative study of DNA Alignment Algorithms and Boosting Performance Using Different Compilation Strategies

Abstract

With the development of next generation sequencing technologies, the requirement of higher performance from DNA and Protein sequence alignment algorithms has become even greater. This work is a systematic comparison of different compilation strategies for two common DNA or Protein sequence alignment algorithms, Needleman-Wunsch and Smith-Waterman, using Python programming language. It aims to investigate the performance benefits of already widely used Biopython’s pairwise alignment module versus different compilation approaches of an in-house software. It is shown that using Numba just-in-time compiler provide greater performance overall in comparison to PyPy and Cython compilers or the Biopython module. This work may increase the efficiency of software prototyping where large-scale sequence alignment is necessary.

Keywords

References

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Details

Primary Language

English

Subjects

Bioinformatic Methods Development , Sequence Analysis

Journal Section

Research Article

Authors

Osman Doluca ^*
0000-0003-0412-6148
Türkiye

Publication Date

December 30, 2024

Submission Date

July 6, 2024

Acceptance Date

December 3, 2024

Published in Issue

Year 2024 Volume: 45 Number: 4

DOI

https://doi.org/10.17776/csj.1511642

IZ

https://izlik.org/JA99XA34GN

Cite

RIS / Bibtex

APA

Doluca, O. (2024). A Comparative study of DNA Alignment Algorithms and Boosting Performance Using Different Compilation Strategies. Cumhuriyet Science Journal, 45(4), 663-667. https://doi.org/10.17776/csj.1511642

A Comparative study of DNA Alignment Algorithms and Boosting Performance Using Different Compilation Strategies

A Comparative study of DNA Alignment Algorithms and Boosting Performance Using Different Compilation Strategies

Abstract

Keywords

DNA Hizalama Algoritmalarının Karşılaştırılmalı Çalışması ve Farklı Derleme Stratejileri ile Performans İyileştirmesi

Öz

Anahtar Kelimeler

References

Details

Primary Language

Subjects

Journal Section

Authors

Publication Date

Submission Date

Acceptance Date

Published in Issue

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