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README.md

README.md

TOPCONS2

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)

Description

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.

Reference

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

Installation and usage:

  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
    

    You may need to update the BLAST database for uniref90 by the script install_blastdb.sh with the following command:

     ./install_blastdb.sh database
    
  4. Install dependencies if not installed

    • Cmake (for installation of modhmm, e.g. sudo apt-get install cmake)
    • perl-Moose (e.g. sudo apt-get install perl-Moose)
    • bioperl-1.6.924 (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 kalign)
    • hmmer3.0 (note that hmmscan should be compatible with the pfam database otherwise, you may encounter format incompatible problem http://hmmer.org/download.html)
    • Gnuplot (e.g. sudo apt-get install gnuplot)
    • Java (make sure that the command java is in the PATH, e.g. sudo apt-get install default-jre)
    • convert from ImageMagick (e.g. sudo apt-get install imagemagick)
    • xsltproc (e.g. sudo apt-get install xsltproc)
    • gengetopt (e.g. sudo apt-get install gengetopt)
    • 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 TOPCONS2 with Docker

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

     unzip topcons2_database.zip
    

    and saved as /data/topcons2_database

    Update the BLAST database for uniref90 by the script install_blastdb.sh with the following command:

     ./install_blastdb.sh /data/topcons2_database/blast
    
  2. Pull the Docker image by

     docker pull nanjiang/topcons2
    

    or you can also build the Docker image locally by

     docker build -t topcons2 .
    

    within the cloned folder, i.e. TOPCONS2/

  3. Run Docker container by

     docker run -v /data/topcons2_database:/data/topcons2_database -it nanjiang/topcons2
    
  4. Test run

     cd /app/topcons2/test
    
     ../run_topcons2.sh one_seq.fasta -outpath rst1
    

    The result will be available at rst1/one_seq/seq_0

    If you want to run TOPCONS2 Docker from outside of the container, suppose you want to output the result to the folder /scratch, then start the container by

     docker run -e USER_ID=$(id -u $USER) -v /data/topcons2_database:/data/topcons2_database -v /scratch:/scratch -it  --name topcons2 -d nanjiang/topcons2
    

    Now you can test run the TOPCONS2 using the example sequence provided in the package by

     docker exec --user user topcons2 script /dev/null -c "/app/topcons2/run_topcons2.sh /app/topcons2/test/one_seq.fasta -outpath  /scratch/rst1"
    

    To use you own sequence, you can copy your query sequence, e.g. yourseq.fasta to /scratch and then run the following command in the shell terminal

     docker exec --user user topcons2 script /dev/null -c "/app/topcons2/run_topcons2.sh /scratch/yourseq.fasta -outpath  /scratch/rst_yourseq"
    

    The prediction result will be output to /scratch/rst_yourseq given successful run.

    Note also that the output files are owned by your current user, i.e. $USER

Run TOPCONS2 with Singularity

You can also run TOPCONS2 with Singularity

  1. Database preparation: do the same as step 1 for when running with Docker.

  2. Pull the Docker image by

     singularity pull docker://nanjiang/topcons2
    
  3. Suppose you have saved the database at /data/topcons2_database and you have a user writable folder /scratch, then you can run TOPCONS2 with the following command

     singularity exec  -B /data:/data -B /scratch:/scratch topcons2.img /app/topcons2/run_topcons2.sh /app/topcons2/test/one_seq.fasta -outpath /scratch/rst1
    

    The prediction result will be output to /scratch/rst1 given successful run.

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

    ../run_octopus.sh -outpath rst2 multiple_seqs.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

    ../run_octopus.sh -outpath rst2 -RM multiple_seqs.fasta

Run only the sub-predictors OCTOPUS and SPOCTOPUS using Docker

Run OCTOPUS and SPOCTOPUS using Docker is similar to run the whole TOPCONS2 workflow.

start the container by (assume you have the write permission to the folder /scratch)

    docker run -e USER_ID=$(id -u $USER) -v /data/topcons2_database:/data/topcons2_database -v /scratch:/scratch -it  --name topcons2 -d nanjiang/topcons2

And make your test run by

    docker exec --user user topcons2 script /dev/null -c "/app/topcons2/run_octopus.sh /app/topcons2/test/one_seq.fasta -outpath  /scratch/rst2"