comparison tools/protein_analysis/tmhmm2.xml @ 6:a290c6d4e658

Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository

5:0f1c61998b22

<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.6">
    <description>Find transmembrane domains in protein sequences</description>
    <command interpreter="python">
      tmhmm2.py 8 $fasta_file $tabular_file
      ##I want the number of threads to be a Galaxy config option...
    </command>

**References**

Krogh, Larsson, von Heijne, and Sonnhammer.
Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes.
J. Mol. Biol. 305:567-580, 2001.

Sonnhammer, von Heijne, and Krogh.
A hidden Markov model for predicting transmembrane helices in protein sequences.
In J. Glasgow et al., eds.: Proc. Sixth Int. Conf. on Intelligent Systems for Molecular Biology, pages 175-182. AAAI Press, 1998.

    </help>
</tool>

6:a290c6d4e658

<tool id="tmhmm2" name="TMHMM 2.0" version="0.0.7">
    <description>Find transmembrane domains in protein sequences</description>
    <command interpreter="python">
      tmhmm2.py 8 $fasta_file $tabular_file
      ##I want the number of threads to be a Galaxy config option...
    </command>

**References**

Krogh, Larsson, von Heijne, and Sonnhammer.
Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes.
J. Mol. Biol. 305:567-580, 2001.
http://dx.doi.org/10.1006/jmbi.2000.4315

Sonnhammer, von Heijne, and Krogh.
A hidden Markov model for predicting transmembrane helices in protein sequences.
In J. Glasgow et al., eds.: Proc. Sixth Int. Conf. on Intelligent Systems for Molecular Biology, pages 175-182. AAAI Press, 1998.
http://www.ncbi.nlm.nih.gov/pubmed/9783223

http://www.cbs.dtu.dk/services/TMHMM/

    </help>
</tool>