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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
