DNA Statistics plugin

DNA Statistics plugin provides exportable statistics reports for various UGENE components

In the current version DNA Statistics plugins provides only "Alignment Grid Profile" report. The Alignment Grid Profile shows positional amino acid or nucleotide counts highlighted according to the frequency of symbols in a row.

The original idea for 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 Alignment editor and use "Statistics->Align" item in popup menu.

The dialog will appear:

Here the brief description for options used in dialog

• Profile mode: counts/percents - select percents to have scores shown as percents in report.
  
  
• Show scores for gaps - check this item if you want gap characters ('-') statistics to be shown in report
  
  
• Show symbols not used in alignment - if a symbol is not used in alignment at all it won't be shown in report. Check this item to make all symbols of alignment alphabet reported.
  
  
• Skip gaps in consensus position increments - consensus ruler configuration. If checked the gaps in consensus will not lead to ruler increments.
  
  
• Save profile to file - allows to save profile to file in HTML or CSV format. The CSV format is convenient for futher processing in worksheets editors like Excel

The result profile in HTML mode: