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

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

doi:10.29130/dubited.898519

TR EN

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

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

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.

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Details

Primary Language

English

Subjects

Engineering

Journal Section

Research Article

Authors

Nursel Söylemez Milli ^*
0000-0003-3610-2706
Türkiye

İsmail Hakkı Parlak This is me
0000-0001-8695-9471
Türkiye

Ercan Selçuk Ünlü
0000-0003-0097-1125
Türkiye

Mehmet Milli
0000-0002-0759-4433
Türkiye

Omer Eren
0000-0001-5650-1320
Türkiye

Publication Date

October 31, 2021

Submission Date

March 22, 2021

Acceptance Date

April 26, 2021

Published in Issue

Year 2021 Volume: 9 Number: 5

DOI

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

IZ

https://izlik.org/JA93MT25EB

APA

Söylemez Milli, N., Parlak, İ. H., Ünlü, E. S., Milli, M., & Eren, O. (2021). A Bioinformatics-Based Approach for Designing Primer Sets in Determination of Meat Specificity. Duzce University Journal of Science and Technology, 9(5), 1669-1675. https://doi.org/10.29130/dubited.898519

AMA

1.Söylemez Milli N, Parlak İH, Ünlü ES, Milli M, Eren O. A Bioinformatics-Based Approach for Designing Primer Sets in Determination of Meat Specificity. DUBİTED. 2021;9(5):1669-1675. doi:10.29130/dubited.898519

Chicago

Söylemez Milli, Nursel, İsmail Hakkı Parlak, Ercan Selçuk Ünlü, Mehmet Milli, and Omer Eren. 2021. “A Bioinformatics-Based Approach for Designing Primer Sets in Determination of Meat Specificity”. Duzce University Journal of Science and Technology 9 (5): 1669-75. https://doi.org/10.29130/dubited.898519.

EndNote

Söylemez Milli N, Parlak İH, Ünlü ES, Milli M, Eren O (October 1, 2021) A Bioinformatics-Based Approach for Designing Primer Sets in Determination of Meat Specificity. Duzce University Journal of Science and Technology 9 5 1669–1675.

IEEE

[1]N. Söylemez Milli, İ. H. Parlak, E. S. Ünlü, M. Milli, and O. Eren, “A Bioinformatics-Based Approach for Designing Primer Sets in Determination of Meat Specificity”, DUBİTED, vol. 9, no. 5, pp. 1669–1675, Oct. 2021, doi: 10.29130/dubited.898519.

ISNAD

Söylemez Milli, Nursel - Parlak, İsmail Hakkı - Ünlü, Ercan Selçuk - Milli, Mehmet - Eren, Omer. “A Bioinformatics-Based Approach for Designing Primer Sets in Determination of Meat Specificity”. Duzce University Journal of Science and Technology 9/5 (October 1, 2021): 1669-1675. https://doi.org/10.29130/dubited.898519.

JAMA

1.Söylemez Milli N, Parlak İH, Ünlü ES, Milli M, Eren O. A Bioinformatics-Based Approach for Designing Primer Sets in Determination of Meat Specificity. DUBİTED. 2021;9:1669–1675.

MLA

Söylemez Milli, Nursel, et al. “A Bioinformatics-Based Approach for Designing Primer Sets in Determination of Meat Specificity”. Duzce University Journal of Science and Technology, vol. 9, no. 5, Oct. 2021, pp. 1669-75, doi:10.29130/dubited.898519.

Vancouver

1.Nursel Söylemez Milli, İsmail Hakkı Parlak, Ercan Selçuk Ünlü, Mehmet Milli, Omer Eren. A Bioinformatics-Based Approach for Designing Primer Sets in Determination of Meat Specificity. DUBİTED. 2021 Oct. 1;9(5):1669-75. doi:10.29130/dubited.898519

Et Özgüllüğünün Belirlenmesinde Primer Setlerinin Tasarımına Yönelik Biyoinformatik Tabanlı Bir Yaklaşım

Abstract

Keywords

Project Number

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

Abstract

Keywords

Supporting Institution

Project Number

Thanks

References

Details

Primary Language

Subjects

Journal Section

Authors

Publication Date

Submission Date

Acceptance Date

Published in Issue

DOI

IZ

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