GeneScanner

GeneScanner is a mutation analysis pipeline for aligned sequences. It reads nucleotide, protein, or both types of FASTA alignments and produces:

  • Per-position mutation summaries with synonymous vs. non-synonymous classification.

  • Detection of protein mutations types and location.

  • Group-wise comparisons.

The function can be accessed by expanding the ‘Analysis’ section on the main contents page.

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Alternatively, it can be accessed following a query by clicking the ‘GeneScanner’ button at the bottom of the results table. Isolates returned from the query will be automatically selected within the GeneScanner interface.

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Select the isolate ids to include a sequence to analyse against. This can either be a pre-defined locus selected from the locus list, or you can paste in your own sequence. This can be either a DNA or protein sequence.

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Choose whether to perform a nucleotide or protein analysis (or both). You can also select one of the sequence ids in your list to be the reference sequence, otherwise the first sequence will be used.

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Click ‘Submit’ to start the analysis.

The main output is an Excel file. See the GeneScanner documentation at https://github.com/jeju2486/GeneScanner/wiki/GeneScanner for details.

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