X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fcalculations%2Fpairwise.html;h=48cebdf392adb174f1b50e33a025a34fca8f3d75;hb=601a323b3e90e2320c52d8b03aba55b1c535a9d0;hp=36c00b1ff685d2b9c4e35258fd4a0312963164fe;hpb=3396e9f33cf3a16a7f38f5163cd057df4b859e7e;p=jalview.git diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html index 36c00b1..48cebdf 100755 --- a/help/html/calculations/pairwise.html +++ b/help/html/calculations/pairwise.html @@ -1,20 +1,40 @@ - -Pairwise Alignment - -

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 + +

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.

+

 

+ +