X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fpairwise.html;h=5ae111e9820e8133ee90b7501299b2dda5e830f5;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=fd210ea7420e38c8dacf563695d9776fe06c4807;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html index fd210ea..5ae111e 100755 --- a/help/html/calculations/pairwise.html +++ b/help/html/calculations/pairwise.html @@ -1,38 +1,48 @@ -Pairwise Alignment + --> + +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 (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.

+