A Bioinformatics-Based Approach for Designing Primer Sets in Determination of Meat Specificity

Year 2021, , 1669 - 1675, 31.10.2021

Nursel Söylemez Milli , İsmail Hakkı Parlak Ercan Selçuk Ünlü , Mehmet Milli Omer Eren

https://doi.org/10.29130/dubited.898519

Abstract

Polymerase chain reaction (PCR) and its derivatives are one of the most widely used DNA-based methods in species determination studies in meat and meat products. Chromosomal or mitochondrial genes of the species can be targeted in PCR-based analyzes used in species detection studies. Many researchers are able to realize oligonucleotide differences between species through online alignment programs on mitochondrial DNA. Using chromosomal DNA would provide more concise results in quantification studies. However, determining the marker regions for genomic DNA is challenging due to the large size of the chromosomes. Bioinformatics approaches are available for selected applications. However, using those approaches requires intensive knowledge of computer science, molecular biology, and bioinformatics in addition to high computational power. In this study, a pipeline is presented that will provide a user-friendly approach to be adopted by facilities where contamination analyzes are routinely performed.

Keywords

Sequence alignment, Bioinformatics, Biocomputing, Food quality

Supporting Institution

BAİBÜ-BAP

Project Number

2017.09.04.1123

Thanks

This study was supported by Bolu Abant İzzet University Scientific Research Projects. In addition the authors would like to thank the Scientific, Industrial and Technological Application and Research Center (STARC) of Bolu Abant İzzet Baysal University for utilization of laboratories.

Et Özgüllüğünün Belirlenmesinde Primer Setlerinin Tasarımına Yönelik Biyoinformatik Tabanlı Bir Yaklaşım

Abstract

Polimeraz zincir reaksiyonu (PCR) ve türevleri, et ve et ürünlerinde tür belirleme çalışmalarında en yaygın kullanılan DNA bazlı yöntemlerden biridir. Tür tespit çalışmalarında kullanılan PCR tabanlı analizlerde türlerin kromozomal veya mitokondriyal genleri hedeflenebilir. Birçok araştırmacı, mitokondriyal DNA üzerindeki çevrimiçi hizalama programları aracılığıyla türler arasındaki oligonükleotid farklılıklarını gerçekleştirebilmektedir. Kromozomal DNA kullanmak, kantifikasyon çalışmalarında daha kısa sonuçlar sağlayacaktır. Bununla birlikte, genomik DNA için işaretleyici bölgelerin belirlenmesi, kromozomların büyüklüğünden dolayı zordur. Biyoinformatik yaklaşımlar, seçilmiş uygulamalar için mevcuttur. Ancak, bu yaklaşımları kullanmak, yüksek hesaplama gücüne ek olarak yoğun bilgisayar bilimi, moleküler biyoloji ve biyoinformatik bilgisi gerektirir. Bu çalışmada, kontaminasyon analizlerinin rutin olarak yapıldığı tesisler tarafından benimsenmesi için kullanıcı dostu bir yaklaşım sağlayacak bir kod akışı sunulmuştur.

Keywords

Sekans hizalama, Biyoinformatik, Biyo-hesaplama, Gıda kalitesi

Project Number

2017.09.04.1123

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