X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Fconsensus.html;h=12d832fb5b5c8cba9d7fc4fbe0ab4d2ef4eb050d;hb=dfa04e77181fccfa6229ffef1591fc9c622d9b39;hp=ce11687ec338ca3f8d3e8063dd70ba02669e4a1e;hpb=c0a695cebfd9a86be228472be431096fa9dc281d;p=jalview.git diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html index ce11687..12d832f 100644 --- a/help/html/calculations/consensus.html +++ b/help/html/calculations/consensus.html @@ -1,13 +1,47 @@ - -Alignment Consensus Annotation - -

Alignment Consensus Annotation

-

The consensus displayed below the alignment is the percentage of the modal - residue per column. By default this calculation takes includes gaps in column. - You can choose to ignore gaps in the calculation by right clicking on the label - "Consensus" to the left of the consensus bar chart. -

If the modal value is shared by more than 1 residue, a "+" symbol - is used in the display for the simple reason that it is not possible to display - multiple characters in a single character space. - - + + +Alignment Consensus Annotation + +

Alignment Consensus Annotation

+

The consensus displayed below the alignment is the percentage of the modal + residue per column. By default this calculation takes includes gaps in column. + You can choose to ignore gaps in the calculation by right clicking on the label + "Consensus" to the left of the consensus bar chart. +

If the modal value is shared by more than 1 residue, a "+" symbol + is used in the display for the simple reason that it is not possible to display + multiple characters in a single character space. +

Copying the consensus sequence

+

Select the "Copy Consensus Sequence" entry from +the consensus annotation label to copy the alignment's consensus sequence to the +clipboard. + +

Sequence logo

+ By clicking on the label you can also activate the sequence logo. It + indicates the relative amount of residues per column which can be + estimated by it's size in the logo. The tooltip of a column gives the + exact numbers for all occuring residues. +
If columns of the alignment are very diverse, then it can + sometimes be difficult to see the sequence logo - in this case, right + click on the annotation row label and select + Normalise Consensus Logo to scale all columns of the + logo to the same height. +

+ +