Meta-Sezgisel Tabanlı Clustal-SA Algoritmasını Kullanarak DNA Sekanslarında Çoklu Dizi Hizalama

Year 2024, Volume: 14 Issue: 2, 544 - 562, 01.06.2024

Hatic Erdirik , Abdullah Ammar Karcıoğlu , Bahattin Tanyolaç , Hasan Bulut

https://doi.org/10.21597/jist.1404898

Abstract

Biyoinformatik, biyolojik verilerin analizi ve kalıtsal ilişkilerin ortaya çıkarılması için matematik, biyoloji ve bilgisayar bilimlerini birleştiren bir disiplindir. Bu alandaki en kritik görevlerden biri, biyolojik dizilerin hizalanmasıyla ilgili olan dizi hizalama problemini çözmektir. Ancak, biyolojik verilerin hızla artması, bu problemi manuel olarak çözülemez hale getirmiş ve bilgisayar sistemlerinin biyoinformatikte daha yaygın bir şekilde kullanılmasına yol açmıştır. Bu çalışmada, mevcut Clustal algoritması ve benzetimli tavlama algoritması kullanılarak yeni bir dizi hizalama algoritması önerilmiştir. Clustal algoritmasının hız avantajını kullanarak ve benzetimli tavlama algoritmasını entegre ederek, Clustal'ın aç gözlü yaklaşımından uzaklaşılarak optimal hizalama skoru elde etmek amaçlanmıştır. Geliştirilen algoritmanın başarısını değerlendirmek için SP (Çiftlerin Toplamı) puanlama sistemi kullanılmış ve hizalama sonucunda sütun eşleşme sayısı dikkate alınmıştır. Elde edilen sonuçlar, geliştirilen algoritmanın aynı uzunluktaki dizi veri kümeleri üzerinde ClustalW programından daha iyi performans gösterdiğini, MUSCLE programına göre ise bazı veri setlerinde daha başarılı olduğu veya yakın sonuçlar verdiğini ortaya koymuştur. Bu gelişme, biyoinformatik alanında dizi hizalama problemini çözmek için yeni ve daha etkili bir yaklaşımın potansiyelini vurgulamaktadır. Gelecekte, bu tür geliştirmelerin biyolojik veri analizi alanında daha geniş bir uygulama alanı bulabileceği düşünülmektedir.

Keywords

Çoklu dizi hizalama, Sezgisel Yaklaşım, Clustal Algoritması, Benzetimli Tavlama, Biyoinformatik

Supporting Institution

Ege Üniversitesi Bilimsel Araştırma Projeleri Koordinatörlüğü

Project Number

FOA-2020-20981

Thanks

Bu çalışma Ege Üniversitesi BAP koordinatörlüğü tarafından FOA-2020-20981 kodlu “Cicer ve Lens türlerinin kloroplast DNA dizilerinin Next Generation Sequencing ile sekanslanması ve genom organizasyonlarının belirlenerek karşılaştırmalı genom analizlerinin gerçekleştirilmesi” isimli proje kapsamında desteklenmiştir.

Multiple Sequence Alignment for DNA Sequences by Using Meta-Heuristic Based Clustal-SA Algorithm

Abstract

Bioinformatics is a discipline that combines mathematics, biology and computer science to analyze biological data and reveal genetic relationships. One of the most critical tasks in this field is to solve the sequence alignment problem, which is related to the alignment of biological sequences. However, the rapid increase in biological data has made this problem unsolvable manually and led to the more widespread use of computer systems in bioinformatics. In this study, a new sequence alignment algorithm is proposed using the existing Clustal algorithm and simulated annealing algorithm. By using the speed advantage of the Clustal algorithm and integrating the simulated annealing algorithm, it is aimed to obtain an optimal alignment score by moving away from the greedy approach of Clustal. To evaluate the success of the developed algorithm, the SP (Sum of Pairs) scoring system was used and the number of column matches as a result of the alignment was taken into account. The results obtained revealed that the developed algorithm performed better than the ClustalW program on sequence data sets of the same length, and was more successful or gave similar results on some data sets compared to the MUSCLE program. This development highlights the potential of a new and more effective approach to solving the sequence alignment problem in bioinformatics. It is thought that in the future, such developments may find wider application in the field of biological data analysis.

Keywords

Multiple Sequence Alignment, Heuristic Approach, Clustal Algorithm, Simulated Annealing, Bioinformatics

Supporting Institution

Ege University Scientific Research Projects Coordinatorship

Project Number

FOA-2020-20981

Thanks

This study was supported by Ege University BAP coordinatorship within the scope of the project titled "Sequencing of chloroplast DNA sequences of Cicer and Lens species by Next Generation Sequencing and performing comparative genome analysis by determining genome organizations" with the code FOA-2020-20981.

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