X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fpairwise.html;h=10902530eb1b9cf12545f462b7906c34087c1080;hb=b3a111ba6d4c239f39d430997fc470ef9008748d;hp=26a47b6a6a364ae980650774cf55d4df422bb7c0;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html index 26a47b6..1090253 100755 --- a/help/html/calculations/pairwise.html +++ b/help/html/calculations/pairwise.html @@ -1,37 +1,58 @@ -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 displays the alignments in a text format, for + example:

+

+ 

+    FER1_SPIOL/5-13 TTMMGMAT

+                    |. .. ||

+    FER1_MESCR/5-15 TAALSGAT
+
+ shows the aligned sequences, where '|' links identical residues, and + (for peptide) '.' links residues that have a positive PAM250 score. +

The window also shows information about the alignment such as + alignment score, length and percentage identity between the + sequences.

+

A button is also provided to allow you to view the sequences as + an alignment.