Mercurial > repos > bgruening > infernal
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author | bgruening |
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date | Tue, 22 Apr 2014 13:56:22 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Tue Apr 22 13:56:22 2014 -0400 @@ -0,0 +1,67 @@ +================================================ +Galaxy wrapper for Infernal prediction tools +================================================ + +Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases +for RNA structure and sequence similarities. It is an implementation of a special +case of profile stochastic context-free grammars called covariance models (CMs). +A CM is like a sequence profile, but it scores a combination of sequence consensus +and RNA secondary structure consensus, so in many cases, it is more capable of +identifying RNA homologs that conserve their secondary structure more than their +primary sequence. + +This wrapper is copyright 2013 by: + * Bjoern Gruening + + +This prepository contains wrapper for the Infernal_ command line tool. + +.. _Infernal: http://infernal.janelia.org/ + + +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). + + +============ +Installation +============ + +Please install Infernal and the tool wrappers with the Galaxy Tool Shed from + +http://toolshed.g2.bx.psu.edu/view/bgruening/infernal + + +======= +History +======= + + - v1.1.0: Initial public release + + +Bug Reports +=========== + +You can file an issue here https://github.com/bgruening/galaxytools/issues or ask +us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE.