X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fquality.html;h=c321e6b3838ffefda63341d8f448e4cb672cf064;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/calculations/quality.html b/help/html/calculations/quality.html index e18e273..c321e6b 100755 --- a/help/html/calculations/quality.html +++ b/help/html/calculations/quality.html @@ -1,18 +1,52 @@ + * 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 +

+

Alignment Quality is one of the automatically calculated + quantitative alignment annotations displayed below the columns of a + multiple sequence alignment (and can be used to shade the + alignment). It is an ad-hoc 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 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.

+ +

+ 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 + conserved BLOSUM62 score (which is higher). This value is normalised + for each column, and then plotted on a scale from 0 to 1. +

+

Multiple alignment algorithms using the BLOSUM 62 substition + matrices should, in theory, maximise alignment quality for an + un-gapped alignment, and locally maximise quality for gapped + alignments.

+ +