Variantis

Variation and Alignment Reporter for Sequences

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About Variantis

Variantis is a user-friendly platform designed for calculating transition and transversion ratios in DNA sequences. It provides a comprehensive matrix for comparative analysis and offers detailed insights into individual nucleotide changes.

Whether you're a researcher, student, or bioinformatics enthusiast, Variantis simplifies the process of analyzing sequence variations, making it accessible to users of all skill levels.

Visit Variantis

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Key Features

1. Transition and Transversion Analysis

• Calculate transition (Ti) and transversion (Tv) ratios for DNA sequences.
• Generate a nucleotide matrix for comparative analysis.
• Colour coded alignment for individual pairs.
• Summary matrices of the all the sequences.

2. User-Friendly Interface

• Intuitive design for easy navigation and file upload.
• Customizable parameters for advanced users.

3. Flexible Input Options

• Supports FASTA format files with extensions: .fasta, .fas, .fa, .fna, .ffn, .frn.
• Allows users to adjust gap open and gap extend parameters for alignment.

4. Automatic Algorithm Selection

• Automatically selects the optimal alignment algorithm based on sequence length:
  • EMBOSS Needle for sequences ≤ 3,000 bases.
  • EMBOSS Stretcher for sequences > 3,000 bases.
• Rejects files with sequences exceeding 10,000 bases to ensure optimal performance.

5. Detailed Results

• Provides alignment files, processed FASTA files, and nucleotide matrices for download.
• Visualizes individual nucleotide changes for in-depth analysis.

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How It Works

1. Upload Your File

   • Input a FASTA file containing DNA sequences for analysis.
   • Ensure the file meets the requirements:
     • Minimum of two sequences.
     • Maximum file size of 10MB.

2. Customize Parameters (Optional)

   • Adjust PSA Program, Gap Open, and Gap Extend values to suit your analysis needs.

3. Submit and Analyze

   • Variantis processes the file, aligns sequences, and calculates transition/transversion ratios.

4. View and Download Results

   • Access alignment files, nucleotide matrices, and transition-transversion ratios for further analysis.

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Why Choose Variantis?

• Accurate and Reliable: Built on robust algorithms for precise sequence analysis.
• Accessible: Designed for users with varying levels of bioinformatics expertise.
• Efficient: Automates complex calculations, saving time and effort.
• Insightful: Provides detailed outputs for comprehensive sequence analysis.

Disclaimer:
The FASTA file sample_2_mega.fasta in the example_data folder is not covered by the same GPL-3.0 license as the source code.
This file is dedicated to the public domain under CC0.

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Get Started

Explore Variantis today and unlock new insights into your DNA sequence data. Whether you're analyzing small datasets or large genomic sequences, Variantis is your go-to tool for variation and alignment reporting.

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Contact

For questions, feedback, or support, please click here.

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License

This project is licensed under the GNU General Public License v3.0 (GPLv3).

© 2025 SharmaG-omics. All rights reserved where applicable.

This project includes the PSA module, which is also licensed under GPLv3.