X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Fconsensus.html;h=c1b276d072218212584a231f7bf4b0e5ab71731b;hb=5160a2b12eaed0e6fb398ec3ff3805e1630b9b83;hp=74bf247c264112a8a6d10d06993a3dd440694a68;hpb=dc507a79f5eb7837ec52343686e84f9d4b56f0fc;p=jalview.git diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html index 74bf247..c1b276d 100644 --- a/help/html/calculations/consensus.html +++ b/help/html/calculations/consensus.html @@ -1,41 +1,75 @@ -
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. +
+ Alignment Consensus Annotation +
+The consensus displayed below the alignment is the percentage + of the modal residue per column. By default this calculation + includes gaps in columns. 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 its size in the logo. The tooltip of a column gives the + exact numbers for all occurring residues. +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. - +
+ Group Consensus
If sequence groups have
+ been defined, then selecting option 'Group Consensus' in the Annotations menu will
+ result in Consensus being calculated for each group, as well as the
+ alignment as a whole.
+
+ cDNA Consensus +
+ A + Split Frame View of cDNA and + Protein alignments will show the consensus for cDNA below the protein + alignment. +