X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Fcalculations%2Fpairwise.html;h=10902530eb1b9cf12545f462b7906c34087c1080;hb=14d7fc7b354d68634fdb65c20ace15741a5b685f;hp=4ad69ca6f9930823a1e77d9798e8e6cfc90a7937;hpb=6fa9683bef52d6709abb81840681e4fa452cafe7;p=jalview.git diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html index 4ad69ca..1090253 100755 --- a/help/html/calculations/pairwise.html +++ b/help/html/calculations/pairwise.html @@ -1,5 +1,58 @@ - - -Tree - - + + + +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 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.

+ +