X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fpairwise.html;h=4b9cf684524794fe566c6fe797ec072b34893384;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=795450b3f3977954346829230587bf7768c0926f;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html index 795450b..4b9cf68 100755 --- a/help/html/calculations/pairwise.html +++ b/help/html/calculations/pairwise.html @@ -1,37 +1,48 @@ -Pairwise Alignment + * 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.

-

 

+

+ 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.

+