X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Fconsensus.html;h=c1b276d072218212584a231f7bf4b0e5ab71731b;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html index e18e273..c1b276d 100644 --- a/help/html/calculations/consensus.html +++ b/help/html/calculations/consensus.html @@ -1,18 +1,75 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> + +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 + 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. +
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. + +

+ 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. +
This may provide additional information on mutations in DNA + that is not visible in the peptide alignment. + +