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Repository hmmer_nhmmer
Name: hmmer_nhmmer
Owner: iuc
Synopsis: Wrapper for hmmer3 application nhmmer
HMMER is used for searching sequence databases for homologs of protein
sequences, and for making protein sequence alignments. It implements
methods using probabilistic models called profile hidden Markov models
(profile HMMs).
Content homepage: http://hmmer.org/
Type: unrestricted
Revision: 7:b28e8ed99424
This revision can be installed: True
Times cloned / installed: 321

Repository README files - may contain important installation or license information

Galaxy wrapper for HMMER3

This wrapper is copyright 2015 by Eric Rasche

HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).

Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.

http://hmmer.janelia.org/ http://hmmer.janelia.org/about

Installation

The recommended installation is by means of the toolshed.

History

  • v0.1.1 - hmmscan: add the possibility to scan a built-in hmm profile database
  • v0.1 - Initial public release

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

Name Description Version Minimum Galaxy Version
search a DNA model or alignment against a DNA database (BLASTN-like) 3.3.2+galaxy0 16.01

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