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python wrapper using protein domain to speed up proteinortho
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Requirement, the following softwares and database must be installed
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* python 2.7
* pfam_scan.pl
* hmm database pfam-27.0
* hmmscan 
* proteinortho (version 4.0, 5.+ not supported)
* libboost

Method
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porthoDom is a wrapper around proteinortho version 4.26.
Latter version are currently not supported but we are working on it.

porthoDom performs the domain annotation of your protein sequences or can use 
pre-existing annotation in pfam format

The domain arrangements present in the input protein sequences set are clustered
together based on our new domain similarity distance.

The clusters are used as sub-space of search for orthologous candidates, ie
proteins sequences with similar domain arrangement are grouped together per 
species and proteinortho is runned on these sub-groups.

The results of the different proteinortho runs are gathered together and a 
standard proteinortho output file is created.


Installation
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porthoDom is composed of two parts, a C program computing the pairwise domain
similarity and a python gluing everything together.

For a local installation
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    python install setup.py --user

Be sure that the local installation path is in our python environment path
add  $HOME/.local/lib in PYTHONPATH

    export PYTHONPATH=$HOME/.local/lib/

add the previous line to your bashrc or personal bashrc

    echo "export PYTHONPATH=$HOME/.local/lib/" >> ~/.bashrc

move the local compute_similarity program from bin to a directory where it will
be accessible by the system


If administrator right are provided
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    sudo python install setup.py


How to cite
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Domain similarity based orthology detection, Tristan Bitard-Feildel, Carsten Kemena, Jenny M Greenwood and Erich Bornberg-Bauer

BMC Bioinformatics2015 16:154

http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0570-8