Gemi, an automated, fast, and easy-to-use bioinformatics tool with a user-friendly interface to design primers and probes for polymerase chain reaction (PCR). Gemi accepts multiple aligned and long DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). Gemi can be used for quantitative, real-time and conventional PCR (qPCR, rt-PCR, etc.), and Sanger sequencing. Gemi can parse large dataset of sequences efficiently.

Python source code is available upon request.

Milestone: The tool reached about 3000 downloads sine 2012.

Article
Gemi: PCR primers prediction from multiple alignments. Comparative and functional genomics 2012
PMID: https://www.ncbi.nlm.nih.gov/pubmed/23316117

A great review on designing primer, Gemi, and other tools: Designing degenerate primers: Overview, challenges, and computational methods. Methods in Microbiology. Vol 57, 2025, Pages 73-89; DOI: 10.1016/bs.mim.2025.01.002

Features

  • Easy to use Molecular Biology and microbiology tool
  • Predicts PCR primers from multiple sequence alignments.
  • Supports degenerate primer design.
  • Provides graphical and text-based output.
  • Scalable tool can parse whole genome of virus or bacteria.

Project Samples

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License

GNU General Public License version 3.0 (GPLv3)

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Gemi Web Site

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Additional Project Details

Operating Systems

BSD, Linux, Windows

Intended Audience

Agriculture, Education, Government, Science/Research

User Interface

.NET/Mono, Win32 (MS Windows)

Programming Language

C#

Related Categories

C# Genetic Algorithms, C# Bio-Informatics Software, C# Education Software

Registered

2012-03-21