Designing degenerate primers: Overview, challenges, and computational methods

Dina Kalinina, Syed Hani Abidi

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

This chapter provides an overview of the concepts, challenges, and computational methods for designing degenerate primers, an important tool in molecular biology for amplifying various gene homologues and variable genomes. It also delves into the intricacies of the primer selection problem and provides a step-by-step approach, utilizing three advanced bioinformatics tools such as Gemi and RPrimer to create primers targeting the HSP70 gene in different species. The approach can be used to design degenerate primers for any gene with any intended downstream PCR applications, such as gene amplification, gene identification, molecular diagnostics, etc.

Original languageEnglish
Title of host publicationMethods in Microbiology
PublisherAcademic Press Inc.
DOIs
Publication statusAccepted/In press - 2025
Externally publishedYes

Publication series

NameMethods in Microbiology
ISSN (Print)0580-9517

Keywords

  • Computational methods and tools
  • Degenerate primers
  • PCR
  • Primer design

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

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