X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Fpairwise.html;h=6f27da5ade3655a7756211c47c2788120f7d60a0;hb=59d682209891099d46b960509907c79e3fb276fe;hp=a076b113c26f0fa857ac0286132f4a1c80e658a4;hpb=1693646e78fb0dddebcd94f8bef7e2acd3bdaae0;p=jalview.git diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html index a076b11..6f27da5 100755 --- a/help/html/calculations/pairwise.html +++ b/help/html/calculations/pairwise.html @@ -1,19 +1,37 @@ - -
-Pairwise alignment (Proteins only)
-This calculation is performed on the selected sequences only. Java is not the
- fastest language in the world and aligning more than a handful of sequences
- will take a fair amount of time.
- For each pair of sequences the best global alignment is found using BLOSUM62
- as the scoring matrix. The scores reported are the raw scores. The sequences
- are aligned using a dynamic programming technique and using the following gap
- penalties :
Gap open : 12
- Gap extend : 2
When you select the pairwise alignment option a new window will come up which - will display the alignments in a text format as they are calculated. Also displayed - is information about the alignment such as alignment score, length and percentage - identity between the sequences.
-- - + + +
Pairwise alignment (Proteins only)
+This calculation is performed on the selected sequences only. Java is not the
+ fastest language in the world and aligning more than a handful of sequences
+ will take a fair amount of time.
+ For each pair of sequences the best global alignment is found using BLOSUM62
+ as the scoring matrix. The scores reported are the raw scores. The sequences
+ are aligned using a dynamic programming technique and using the following gap
+ penalties :
Gap open : 12
+ Gap extend : 2
When you select the pairwise alignment option a new window will come up which + will display the alignments in a text format as they are calculated. Also displayed + is information about the alignment such as alignment score, length and percentage + identity between the sequences.
++ +