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Repository infernal
Name: infernal
Owner: bgruening
Synopsis: Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.
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. http://infernal.janelia.org/
Content homepage: http://infernal.janelia.org/
Development repository: https://github.com/bgruening/galaxytools/tree/master/tools/infernal
Link to this repository: https://toolshed.g2.bx.psu.edu/view/bgruening/infernal/3711f654044e
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/infernal
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Repository README files - may contain important installation or license information

Readme files

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.

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.

Contents of this repository

Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Name Description Version Minimum Galaxy Version
Align sequences to a covariance model against a sequence database 1.1.5+galaxy0 16.01
Build covariance models from sequence alignments 1.1.5+galaxy0 16.01
Prepare a covariance model database for cmscan 1.1.5+galaxy0 23.0
Search sequences against collections of covariance models 1.1.5+galaxy0 16.01
Search covariance model(s) against a sequence database 1.1.5+galaxy0 16.01
Summary statistics for covariance model 1.1.5+galaxy0 16.01

Categories
RNA - Utilities for RNA
Sequence Analysis - Tools for performing Protein and DNA/RNA analysis