X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fconsensus.html;h=0476f05ff35122d923e027c6765bb1ae46c8ac65;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=12d832fb5b5c8cba9d7fc4fbe0ab4d2ef4eb050d;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html index 12d832f..0476f05 100644 --- a/help/html/calculations/consensus.html +++ b/help/html/calculations/consensus.html @@ -1,47 +1,68 @@ -Alignment Consensus Annotation + --> + +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. +

+ 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. -

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. -

+

+ 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.