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