3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 <title>Pairwise Alignment</title>
27 <strong>Pairwise alignment (Proteins only)</strong>
30 This calculation is performed on the selected sequences only. Java
31 is not the fastest language in the world and aligning more than a
32 handful of sequences will take a fair amount of time. <br> For
33 each pair of sequences the best global alignment is found using
34 BLOSUM62 as the scoring matrix. The scores reported are the raw
35 scores. The sequences are aligned using a dynamic programming
36 technique and using the following gap penalties :
39 Gap open : 12 <br> Gap extend : 2
41 <p>When you select the pairwise alignment option, a new window
42 will come up which displays the alignments in a text format, for
46 FER1_SPIOL/5-13 TTMMGMAT<br />
48 FER1_MESCR/5-15 TAALSGAT
50 shows the aligned sequences, where '|' links identical residues, and
51 (for peptide) '.' links residues that have a positive PAM250 score.
52 <p>The window also shows information about the alignment such as
53 alignment score, length and percentage identity between the
55 <p>A button is also provided to allow you to view the sequences as