X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fpairwise.html;fp=help%2Fhtml%2Fcalculations%2Fpairwise.html;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=10902530eb1b9cf12545f462b7906c34087c1080;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html deleted file mode 100755 index 1090253..0000000 --- a/help/html/calculations/pairwise.html +++ /dev/null @@ -1,58 +0,0 @@ - - - -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.

- -