X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fquality.html;h=a16193af118c6f701208b0fc58f921e3de327a98;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=33507339ed6a0ab958cbf5809dfbc97f7c6f37b1;hpb=0696cffbccbb537be78d9fc2410589adbcd7be35;p=jalview.git diff --git a/help/html/calculations/quality.html b/help/html/calculations/quality.html index 3350733..a16193a 100755 --- a/help/html/calculations/quality.html +++ b/help/html/calculations/quality.html @@ -1,21 +1,24 @@ + * 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 Quality Annotation

Alignment Quality Annotation

@@ -27,7 +30,7 @@ measure of the likelihood of observing the mutations (if any) in a particular column of the alignment.

More precisely, the quality score is inversely proportional to the -average cost of all pairs of mutations oberved in a particular column +average cost of all pairs of mutations observed in a particular column of the alignment - a high alignment quality score for a column would suggest that there are no mutations, or most mutations observed are favourable. @@ -36,8 +39,8 @@ favourable.

The Algorithm
The quality score is calculated for each column in an alignment by summing, for all mutations, the ratio of the two BLOSUM 62 scores for -a mutation pair and each residue's conservered BLOSUM62 score (which -is higher). This valueis normalised for each column, and then plotted +a mutation pair and each residue's conserved BLOSUM62 score (which +is higher). This value is normalised for each column, and then plotted on a scale from 0 to 1.