X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Fcalculations%2Fpairwise.html;h=10902530eb1b9cf12545f462b7906c34087c1080;hb=14d7fc7b354d68634fdb65c20ace15741a5b685f;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git
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+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
+ 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+ shows the aligned sequences, where '|' links identical residues, and + (for peptide) '.' links residues that have a positive PAM250 score. +
+ |. .. ||
+ FER1_MESCR/5-15 TAALSGAT +
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.
+ +