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. Since Jalview 2.11.4.0, the substitution matrix can be customised via the Calculations Dialog.

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.