🧬 PrimerX

This is a simple shiny app to analyze primers using R programming language. The app includes features to analyze GC-content, hairpin formation, homo-dimers, melting temperature (TM), and import files in various formats.

🛠️ Installation

To run the app locally, you will need to have R and RStudio installed on your machine.

• R
• RStudio

You will also need to install the following R packages:

• shiny
• shinythemes
• primer3
• stringr
• Biostrings
• seqinr

You can install these packages using the Bioconductor installer.

💻 Usage

To launch the app, open the app.R file in RStudio and click the "Run App" button. This will launch the app in your default web browser.

• Input: This tab allows you to input primer sequences and settings for analysis either by pasting the sequence or browsing your file.
• GC-content: Shows the GC-content value of your primer.
• Hairpin Formation: Shows the potential for hairpin formation in the primer sequence.
• Homo-dimer: Shows the potential for homodimerization (self-dimerization) in the primer sequence.
• Tm: Melting temperature (TM) for the primer.

To import files, click on the "Browse" button. This will allow you to select and upload files in FASTA or plain text format. You can also download the results of your primer analysis using the "Download Results" button.

🚀 TODO

Include more tabs for further sequence analysis other than just for primers.

• Display self-dimerization
• ClustalW implementation
• Enrichment analysis
• BLAST