3 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
4 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 <title>Mapping Between Different Sequences</title>
23 <p><strong>Mapping Between Different Sequences</strong></p>
24 <p>A new feature in Jalview 2.3 is the ability to map between sequences in different
25 domains, based on alignment, or by the use of explicit mappings provided by
27 <p>The most familiar mapping is the one used to identify
28 the coordinates corresponding to a displayed sequence when
29 viewing a PDB file associated with a sequence (see
30 <a href="viewingpdbs.html">"Viewing PDB Files"</a>
31 for more information.</p>
32 <p>The newest form of mapping supported by Jalview is the
33 correspondence between DNA and protein sequences. This mapping
34 can be imported directly from EMBL and EMBLCDS database records
35 retrieved by the <a href="seqfetch.html">Sequence Fetcher</a>,
36 and allows sequence features to be mapped directly from Uniprot
37 das sources to their coding region on EMBL sequence records.