X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fcalculations%2Fpairwise.html;h=10902530eb1b9cf12545f462b7906c34087c1080;hb=14d7fc7b354d68634fdb65c20ace15741a5b685f;hp=6f27da5ade3655a7756211c47c2788120f7d60a0;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git diff --git a/help/html/calculations/pairwise.html b/help/html/calculations/pairwise.html index 6f27da5..1090253 100755 --- a/help/html/calculations/pairwise.html +++ b/help/html/calculations/pairwise.html @@ -1,37 +1,58 @@ -
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+ 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.