X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fconservation.html;h=6a14bb118ab209fe1643fa9bec0ff5f235bad2a6;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=7c5953f5337556fa5209b811bcf78bec1e8c27e2;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git diff --git a/help/html/calculations/conservation.html b/help/html/calculations/conservation.html index 7c5953f..6a14bb1 100755 --- a/help/html/calculations/conservation.html +++ b/help/html/calculations/conservation.html @@ -1,44 +1,75 @@ -Alignment Conservation Annotation -

Alignment Conservation Annotation

-

This is an automatically calculated quantitative alignment -annotation which measures the number of conserved physico-chemical -properties conserved for each column of the alignment. Its calculation -is based on the one used in - the AMAS method of multiple sequence alignment analysis :
-

-

-

Conservation is measured as a numerical index reflecting the conservation of - physico-chemical - properties in the alignment: Identities score highest, and the next most - conserved group contain substitutions to amino acids lying in the same physico-chemical - class.

- -

Colouring an alignment by conservation
-Conservation scores can be used to colour an alignment. This is -explained further in the help page for conservation colouring. -

+ * 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 Conservation Annotation + + +

+ Alignment Conservation Annotation +

+

+ This is an automatically calculated quantitative alignment + annotation which measures the number of conserved physico-chemical + properties conserved for each column of the alignment. Its + calculation is based on the one used in the AMAS method of multiple + sequence alignment analysis :
+

+ View an HTML version of the paper +

+

+ Conservation is measured as a numerical index reflecting the + conservation of physico-chemical + properties in the alignment: Identities score highest, and the + next most conserved group contain substitutions to amino acids lying + in the same physico-chemical class. +

+

Conservation is visualised on the alignment or a sequence group + as a histogram giving the score for each column. Conserved columns + are indicated by '*' (score of 11 with default amino acid property + grouping), and columns with mutations where all properties are + conserved are marked with a '+' (score of 10, indicating all + properties are conserved).

+

+ Mousing over a conservation histogram reveals a tooltip which + contains a series of symbols corresponding to the physicochemical + properties that are conserved amongst the amino acids observed at + each position. In these tooltips, the presence of ! implies + that the lack of a particular physicochemical property is conserved + (e.g. !proline). +

+

+ Colouring an alignment by conservation
+ Conservation scores can be used to colour an alignment. This is + explained further in the help page for conservation colouring. +