Variantis is a user-friendly platform for calculating transition and transversion ratios.
It generates a matrix for comparative analysis and provides insights into individual nucleotide changes.
It generates a matrix for comparative analysis and provides insights into individual nucleotide changes.
Instructions
1. Input the file containing fasta sequences you want to compare {.fasta, .fas, .fa, .fna, .ffn,
.frn} . Click here for the default parameters.
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2. If you want to change the default parameters. Click on the custom parameters.
NOTE:
Please ensure the following requirements are met before uploading your file:
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File Format: Uploaded files must be in DNA FASTA format as above displayed in the sample file. Accepted extensions:
.fasta,.fas,.fa,.fna,.ffn,.frn. - Minimum Sequences: The file must contain at least two sequences.
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Since global alignment is performed, ensure that the sequences being compared share a significant level of similarity. Although results will be generated for all sequence pairs,
those with less than 60% identity will be specifically highlighted in the dashboard for further attention. - If EMBOSS Stretcher is selected, make sure the gap open and gap extend are above 1 and whole numbers (NO FLOATS).
- File Size: The maximum file size is 10MB. For larger files, please split them into smaller files before uploading.
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Sequence Length:
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Automatic Algorithm Selection:
- If any sequence exceeds 3,000 bases, the system will automatically switch to the Stretcher algorithm for all sequence comparisons.
- In this case, if your custom gap parameters are below 1:
- Gap Open will default to 16
- Gap Extend will default to 4
- This applies to all sequences in the file, regardless of their individual lengths.
- Files containing sequences longer than 10,000 bases will be rejected.
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Automatic Algorithm Selection: