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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 E. P. Nawrocki, D. L. Kolbe, and S. R. Eddy, Infernal 1.0: Inference of RNA alignments , Bioinformatics 25:1335-1337 (2009), .
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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 download install Infernal and the tool wrappers with the Galaxy Tool Shed:
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30
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31 =============
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32 Miscellaneous
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33 =============
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34
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35 Included in that repository is a CM datatype for INFERNAL 1.1 and TOCKHOLM .
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36 If you need that datatype in an additionl package, I can source it out as separate package. Please contact me in that case.
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37
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1
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38
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39 =======
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40 History
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41 =======
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42
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43 - v1.1.0: Initial public release
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44
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45
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46
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47
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48 ===============================
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49 Wrapper Licence (MIT/BSD style)
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50 ===============================
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51
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52 Permission to use, copy, modify, and distribute this software and its
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53 documentation with or without modifications and for any purpose and
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54 without fee is hereby granted, provided that any copyright notices
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55 appear in all copies and that both those copyright notices and this
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56 permission notice appear in supporting documentation, and that the
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57 names of the contributors or copyright holders not be used in
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58 advertising or publicity pertaining to distribution of the software
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59 without specific prior permission.
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60
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61 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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62 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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63 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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64 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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65 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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66 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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67 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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68 OR PERFORMANCE OF THIS SOFTWARE.
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69
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