Abstract

Designing primers is a challenge for researchers to design primers that can amplify sequence genes. Primer design has several parameters considered, namely primer length, thermal melting temperature (TM), and guanine-cytosine content (GC-content). Therefore, bioinformatics is needed to help design primers more informatively by showing the parameter values of the primer design. One of the programs used to design primers is Primer3Plus. Primer3Plus can create several primer designs. Thus, Primer3Plus requires an expert to choose a primer pair that fits with the primer length, TM, and GC content parameters. This research proposed an improvised method for prioritizing design primer pairs from the Primer3Plus results to obtain the most suitable primer pairs according to the specified parameters. Before being processed into Primer3Plus, the gene sequence is split into several sequences with a length of around 1000bp to suit Sanger Sequencing (SGS). Therefore, the primers designed from each sequence can amplify all parts of the gene sequence. The experiment used the sequence gene Sorghum bicolor phytochrome A (PHYA) gene from the National Center for Biotechnology Information (NCBI) and implemented using Python with the Biopython library. The results get the best pair primers from each sequence based on primer length, TM, and GC content parameters with a product size of 900-1000bp for PCR and sequencing using SGS.

Original languageEnglish
Title of host publicationProceeding - 6th International Conference on Information Technology, Information Systems and Electrical Engineering
Subtitle of host publicationApplying Data Sciences and Artificial Intelligence Technologies for Environmental Sustainability, ICITISEE 2022
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages443-448
Number of pages6
ISBN (Electronic)9798350399615
DOIs
Publication statusPublished - 2022
Event6th International Conference on Information Technology, Information Systems and Electrical Engineering, ICITISEE 2022 - Virtual, Online, Indonesia
Duration: 13 Dec 202214 Dec 2022

Publication series

NameProceeding - 6th International Conference on Information Technology, Information Systems and Electrical Engineering: Applying Data Sciences and Artificial Intelligence Technologies for Environmental Sustainability, ICITISEE 2022

Conference

Conference6th International Conference on Information Technology, Information Systems and Electrical Engineering, ICITISEE 2022
Country/TerritoryIndonesia
CityVirtual, Online
Period13/12/2214/12/22

Keywords

  • Bioinformatics
  • Polymerase Chain Reaction
  • Primer Design
  • Primer3Plus
  • Sanger Sequencing

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