X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fpairwise.html;h=2891f1edab09a49c238989566d28d539ad7ed62f;hb=5f9c8558cfee09b2ba2a13226f5bd4188e299135;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html index e18e273..2891f1e 100755 --- a/help/html/calculations/pairwise.html +++ b/help/html/calculations/pairwise.html @@ -1,18 +1,40 @@ + * 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. + --> +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.

+

 

+ +