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Last update on 04. Dec 2013 .
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How is the consensus calculated?

OCCURRENCE

ARB_NT/SAI/Create SAI using../Consensus ARB_EDIT4/Properties/Consensus definition

 

DESCRIPTION

What to do with gaps?

  • If a column contains only gaps the result will be shown as '='.
  • Define whether to use or to ignore gaps entirely:
    • If you count gaps and the gap frequency exceeds 'threshold for gaps', the result will be shown as '-'.
    • If the switch is 'off', the algorithm will virtually remove all gaps. That means if you have a column with two 'A's and 500 gaps the program thinks of 100% 'A'. (If the switch is 'on', the relative number of 'A's would be 2%)


Simplify using IUPAC

  • Define whether the most frequent base or the IUPAC code (more then one base) should be shown at the particular position by pressing the respective checkbox after the 'simplify' prompt.
  • Characters are used for IUPAC encoding only if their frequency exceeds 'threshold for character'.
  • Example:

    If you have 40% 'A', 10% 'C', 40% 'G' and 10% 'T' and 'threshold for character' is set to 20%, the program looks for a iupac code only for 'A' and 'G'.

  • Note:

    The IUPAC codes are displayed after pressing the 'show IUPAC' button.


Show as upper or lower case?

  • Define whether the character is displayed in upper or lower case or whether a dot is displayed.
  • Define upper and lower limit:
    • If the percentage of a character is above or equal to the upper limit, the character is displayed in upper case.
    • If the percentage of a character is above or equal to the lower limit and below the upper limit, the character is displayed in lower case.
    • Otherwise a dot ('.') is displayed.


 

NOTES

None

 

EXAMPLES

None

 

WARNINGS

IUPAC symbols in source sequences are ignored.

 

BUGS

'consensus.ps (Postscript) ' is broken for more than 10 years now. Seems that nobody ever took a look.