This is the standalone version of web-server http://topcons.net. This software package is supposed to be run on Ubuntu x64 system. It might also work on other Linux boxes but have not been tested.

If you are interested in running TOPCONS2 on other systems, please contact Arne Elofsson (arne@bioinfo.se)

TOPCONS2 is an updated version of the widely used TOPCONS for predicting membrane protein topologies using consensus prediction. It is faster yet more accurate than the old TOPCONS according to our solid benchmarking. Moreover, it predicts not only the trans-membrane helices, but also the location of signal peptide

The software is open source and licensed under the GPL license.

Tsirigos, K.D., Peters, C., Shu, N., Kall, L., Elofsson, A., 2015. The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. Nucleic Acids Res. 43, W401-W407

1. Check out the software from the github by

   $ git clone https://github.com/ElofssonLab/TOPCONS2

2. Download the database for TOPCONS2 from http://topcons.net/static/download/topcons2_database.zip and unzip it by

   $ unzip topcons2_database.zip

3. Change to the folder 'topcons2_webserver' and create a soft link to the downloaded database

   $ ln -s /path/to/the/downloaded/database database

4. Install dependencies if not installed

   • Cmake (for installation of modhmm)
   • perl-Moose (e.g. sudo apt-get install perl-Moose)
   • bioperl (e.g. cpan > install CJFIELDS/BioPerl-1.6.924.tar.gz )
   • biopython (e.g. sudo pip install biopython )
   • IPC (e.g. cpan > install IPC::Run)
   • kalign (e.g. sudo apt-get install kalign2)
   • hmmer3.0 (note that hmmscan should be compatible with the pfam database otherwise, you may encounter format incompatible problem)
   • Gnuplot
   • convert from ImageMagic
   • awk, sort, head

   Note that the commands hmmscan, kalign, gnuplot, convert, sort, awk and head should be in the PATH

5. Install modhmm

   change to the folder 'topcons2_webserver/predictors/source/modhmm'

   $ bash fresh_install.sh /path/to/topcons2_webserver/predictors

6. Test the topcons2 workflow

   change to the folder 'topcons2_webserver/test' and run the following commands

   $ ../workflow/pfam_workflow.py one_seq.fasta rst1 ../tools/blast-2.2.26/ ../database/blast/uniref90.fasta

   $ ../workflow/pfam_workflow.py multiple_seqs.fasta rst2 ../tools/blast-2.2.26/ ../database/blast/uniref90.fasta

   The example results can be found in the folder 'rst_one_seq' and 'rst_multiple_seqs' for the example fasta file one_seq.fasta and multiple_seqs.fasta respectively.

• Description of the output results If the input contains one sequence and the out_path is "one_seq" The tree view of all output files will be

    one_seq/
    ├── seq_0              # if there are more than one sequence in the input
    │   │                  # file, the subfolders will be named as seq_1, seq_2 ... 
    │   ├── DG1.txt
    │   ├── Homology
    │   │   ├── query.fa.total_aligns
    │   │   └── query.top
    │   ├── OCTOPUS
    │   │   ├── NN_PRF_FILES
    │   │   │   └── query.prf  # Detailed network prediction for OCTOPUS
    │   │   └── query.top
    │   ├── PolyPhobius
    │   │   └── query.top
    │   ├── SCAMPI_MSA
    │   │   └── query.top
    │   ├── SPOCTOPUS
    │   │   ├── NN_PRF_FILES
    │   │   │   └── query.nnprf
    │   │   └── query.top
    │   ├── Topcons
    │   │   ├── reliability.final
    │   │   ├── reliability.txt
    │   │   ├── topcons.gnu
    │   │   ├── topcons.large.png
    │   │   ├── topcons.png
    │   │   ├── topcons.top       # the predicted topology for TOPCONS
    │   │   ├── total_image.gnu
    │   │   ├── total_image.large.png
    │   │   └── total_image.png
    │   ├── dg.txt
    │   ├── nicetop.html
    │   ├── philius
    │   │   └── query.top
    │   ├── query.result.txt
    │   ├── seq.fa
    │   └── time.txt
  
    

##Run only the sub-predictors OCTOPUS and SPOCTOPUS If you only need to run OCTOPUS and SPOCTOPUS within the TOPCONS2 package, you need to install the whole package using the procedure described above for TOPCONS2. Then, use the script pfam_workflow_octopus.py.

Examples: change to the folder 'topcons2_webserver/test' and run the following commands

`$ ../workflow/pfam_workflow_octopus.py multiple_seqs.fasta rst1 ../tools/blast-2.2.26/ ../database/blast/uniref90.fasta`

The result of predicted topologies in Fasta format can be found in rst1/multiple_seqs.OCTOPUS.topfa and rst1/multiple_seqs.SPOCTOPUS.topfa

If you do not need the individual output files nor the ANN output, you can run the commands with the "-remove-individual-files" flag, that is

`$ ../workflow/pfam_workflow_octopus.py multiple_seqs.fasta rst1 ../tools/blast-2.2.26/ ../database/blast/uniref90.fasta -remove-individual-files`