X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fstructureconsensus.html;h=e32dd3626a964d67c60b7a32deb6eb104a8d6393;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=ccc249f1c1bddf2ad58243a01f6d56408e172d80;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/help/html/calculations/structureconsensus.html b/help/html/calculations/structureconsensus.html index ccc249f..e32dd36 100755 --- a/help/html/calculations/structureconsensus.html +++ b/help/html/calculations/structureconsensus.html @@ -1,7 +1,7 @@ -Alignment RNA Structure Consensus Annotation -

Alignment RNA Structure Consensus Annotation

+ +Alignment RNA Structure Consensus Annotation + + +

+ Alignment RNA Structure Consensus Annotation +

-

The RNA structure consensus displayed below the alignment is the -percentage of valid base pairs per column. It is calculated in -relation to a secondary structure and just paired columns are -calculated. The canonical Watson-Crick base pairings (A-T/U, G-C) and -the wobble base pair (G-T/U) are regarded as valid pairings.
-The amount of valid base pairs is indicated by the profile in the -Alignment Annotation row.
-By default this calculation includes gaps in columns. You can choose -to ignore gaps in the calculation by right clicking on the label -"StrConsensus" to the left of the structure consensus bar -chart.
- -

Structure logo

-By clicking on the label you can also activate the structure logo. It is very -similar to a sequence logo but counts the numbers of base pairs. There -are two residues per column, the actual column and the interacting -base. The opening bracket is always the one on the left side.
-Like sequence logos the relative amount of a specific base pair can be -estimated by its size in the logo. The tool tip of a column gives the -exact numbers for all occurring valid base pairs. -

+

+ The RNA structure consensus displayed below the alignment is the + percentage of valid base pairs per column. It is calculated in + relation to a secondary structure and just paired columns are + calculated. The canonical Watson-Crick base pairings (A-T/U, G-C) + and the wobble base pair (G-T/U) are regarded as valid pairings.
+ The amount of valid base pairs is indicated by the profile in the + Alignment Annotation row.
By default this calculation + includes gaps in columns. You can choose to ignore gaps in the + calculation by right clicking on the label "StrConsensus" + to the left of the structure consensus bar chart.
+

+ Structure logo +

+ By clicking on the label you can also activate the structure logo. It + is very similar to a sequence logo but counts the numbers of base + pairs. There are two residues per column, the actual column and the + interacting base. The opening bracket is always the one on the left + side. +
Like sequence logos the relative amount of a specific base + pair can be estimated by its size in the logo. The tool tip of a + column gives the exact numbers for all occurring valid base pairs. +