DNA Statistics

The DNA Statistics plugin provides exportable statistical reports.

In the current UGENE version, the DNA Statistics plugin only provides an Alignment Grid Profile report. The Alignment Grid Profile displays positional amino acid or nucleotide counts, highlighted according to the frequency of symbols in a row.

The original idea of the MSA Grid Profile is described in the following paper:

“Alberto Roca, Albert Almada and Aaron C Abajian: ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family, BMC Bioinformatics 2008, 9:554”

Usage example:

Open a sequence alignment in the Alignment Editor and use the Statistics ‣ Generate grid profile context menu item.

The dialog will appear:

Here is a brief description of the options that can be set in the dialog:

  • Profile mode: Counts/Percents — select Percents to have scores shown as percentages in the report.

  • Show scores for gaps — check this item if you want gap character (‘—’) statistics to be displayed in the report.

  • Show scores for symbols not used in alignment — if a symbol is not used in the alignment at all, it won’t be displayed in the report. Check this item to report all symbols of the alignment alphabet.

  • Skip gaps in consensus position increments — consensus ruler configuration. If checked, the gaps in the consensus will not lead to ruler increments.

  • Save profile to file — allows saving the profile to a file in HTML or CSV format. The CSV format is convenient for further processing in spreadsheet editors like Excel.

The resulting profile in HTML mode:

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