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author bgruening
date Tue, 22 Apr 2014 13:56:22 -0400
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1 ================================================
2 Galaxy wrapper for Infernal prediction tools
3 ================================================
4
5 Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases
6 for RNA structure and sequence similarities. It is an implementation of a special
7 case of profile stochastic context-free grammars called covariance models (CMs).
8 A CM is like a sequence profile, but it scores a combination of sequence consensus
9 and RNA secondary structure consensus, so in many cases, it is more capable of
10 identifying RNA homologs that conserve their secondary structure more than their
11 primary sequence.
12
13 This wrapper is copyright 2013 by:
14 * Bjoern Gruening
15
16
17 This prepository contains wrapper for the Infernal_ command line tool.
18
19 .. _Infernal: http://infernal.janelia.org/
20
21
22 The recommended citation for using Infernal 1.1 is E. P. Nawrocki and S. R. Eddy, Infernal 1.1: 100-fold faster RNA homology searches , Bioinformatics 29:2933-2935 (2013).
23
24
25 ============
26 Installation
27 ============
28
29 Please install Infernal and the tool wrappers with the Galaxy Tool Shed from
30
31 http://toolshed.g2.bx.psu.edu/view/bgruening/infernal
32
33
34 =======
35 History
36 =======
37
38 - v1.1.0: Initial public release
39
40
41 Bug Reports
42 ===========
43
44 You can file an issue here https://github.com/bgruening/galaxytools/issues or ask
45 us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev
46
47
48 Licence (MIT)
49 =============
50
51 Permission is hereby granted, free of charge, to any person obtaining a copy
52 of this software and associated documentation files (the "Software"), to deal
53 in the Software without restriction, including without limitation the rights
54 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
55 copies of the Software, and to permit persons to whom the Software is
56 furnished to do so, subject to the following conditions:
57
58 The above copyright notice and this permission notice shall be included in
59 all copies or substantial portions of the Software.
60
61 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
62 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
63 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
64 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
65 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
66 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
67 THE SOFTWARE.