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.
26 <strong>HMMER Menu</strong>
28 <p>This menu is available if hmmbuild tools have been installed and configured in the
29 <a href="../features/preferences.html#hmmer">HMMER Preferences</a> panel.
32 <strong>hmmbuild</strong>
33 <br><br>Run hmmbuild to create a Hidden Markov Model profile of your sequence alignment or sub-groups.
34 <br><br>The consensus sequence for the computed profile is inserted as the first sequence of
35 the alignment (or group) for which hmmbuild is run.
36 <br>Jalview also computes and displays an annotation below the alignment, showing
37 the information content of each column.
38 <br>This is calculated as the sum over residue symbols of
40 match emission probability * log(match emission probability / background frequency) / log(2)
42 where the background frequencies are taken from (tbc: where? not https://www.ebi.ac.uk/uniprot/TrEMBLstats)
44 <li>Edit settings and run...
45 <br><br>Choose whether to run hmmbuild for the whole alignment, or all or selected groups, or both
46 (default is the alignment).
47 <br>Optionally enter a name to give the HMM profile consensus sequence
48 (default is "Alignment" or group name, with "_HMM" appended).
49 <br>Use Reference Annotation: select this option if your alignment has an RF reference annotation,
50 and you wish to constrain the HMM profile to it (hmmbuild option '--hand').
52 <li>hmmbuild with default settings
53 <br><br>Runs hmmbuild for the whole alignment.</li>
56 <strong>hmmalign</strong> and <strong>hmmsearch</strong> require an HMM consensus sequence to be selected first.
57 <br><em>To do this, right-click on the name of an HMM sequence added by hmmbuild, and 'Select HMM'.
58 The alignment will be with respect to the HMM profile for the consensus sequence.</em>
60 <strong>hmmalign</strong>
61 <br><br>Run hmmalign to align selected sequences (or the whole alignment) to a selected HMM profile.
63 <li>Edit settings and run...
64 <br><br>Choose whether to 'trim non-matching termini' - hmmalign option '--trim'.
66 <li>hmmalign with default settings</li>
68 <strong>hmmsearch</strong>
69 <br><br>Run hmmsearch to use an HMM profile as input to search a sequence database.
71 <li>Edit settings and run...
73 <li>tbc: choose database</li>
74 <li>tbc: automatically align</li>
75 <li>tbc: return accessions</li>
76 <li>tbc: number of results</li>
77 <li>tbc: sequence eValue cutoff</li>
78 <li>tbc: domains eValue cutoff</li>
81 <br><li>hmmsearch with default settings</li>
83 <br>Browse to select a local sequence data file to be searched</li>