PaSiMap (Pairwise Similarity Map)

Purpose

The aim of the tool PaSiMap is to map protein sequences as coordinates based on their pairwise similarities.

In order to determine the pairwise similarities, PaSiMap first computes global alignments for each pair of sequences. The similarity of each aligned pair of sequences is then quantified as a number in order to allow the mapping with the multidimensional scaling method cc_analysis

For more details please refer to PaSiMap paper.

How to get started

PaSiMap webserver

The easiest way to use PaSiMap is with our PaSiMap webserver.

Simply submit your query to the webserver and download your results. You can also try out PaSiMap with the example query provided on the webserver.

Local PaSiMap on Linux

Setting up

1. Get PaSiMap from GitHub:

   git clone https://github.com/ksu00/pasimap.git
   

   This results in the directory named pasimap.

   ⚠️ All the following steps will be done from within this pasimap directory.

2. Set up directory structure:

   # In pasimap directory.
   mkdir src/webserver
   mkdir src/webserver/static
   mkdir src/webserver/static/tmp
   

   The directory for each job (contains query, interim results and final results) will have to be located in this tmp directory.

3. Set up Python Virtual Environment:

   ⚠️ Make sure that the correct Python version (Python 3) is active, PaSiMap was developed with Python 3.6.12.

   Install Python package for Virtual Environments:

   pip install virtualenv --user
   

   Create new Virtual Environment for PaSiMap:

   # In pasimap directory.
   python -m venv venv
   

   Activate Virtual Environment for PaSiMap:

   # In pasimap directory.
   source venv/bin/activate
   

   Install packages required by PaSiMap:

   # In pasimap directory.
   pip install -r requirements.txt
   

4. Set up needleall (EMBOSS).

   Download and configure EMBOSS software suite (version 6.6.0) from EMBOSS.

   Add needleall to PATH OR adjust to your needleall path in the following line in run_pipeline.sh (in pasimap directory):

   time needleall -asequence $in_file_path \
   

   Adjust location of substitution matrix to your path in the following line in run_pipeline.sh (in pasimap directory):

   substmat_dir_path=/usr/local/EMBOSS-6.6.0/emboss/data;
   

5. Set up cc_analysis:

   Download binary of cc_analysis.

   Add cc_analysis to to PATH OR adjust to your cc_analysis path in the following line in run_pipeline.sh (in pasimap directory):

   time cc_analysis -dim $dim \
   

Running job

1. Create job directory (e.g. ASDF, but you can name it whatever you want):

   # In pasimap directory.
   mkdir src/webserver/static/tmp/ASDF
   

2. Prepare query:

   # In pasimap directory.
   mkdir src/webserver/static/tmp/ASDF/0_input
   touch src/webserver/static/tmp/ASDF/0_input/dim.txt
   touch src/webserver/static/tmp/ASDF/0_input/state.txt
   touch src/webserver/static/tmp/ASDF/0_input/input.txt
   touch src/webserver/static/tmp/ASDF/0_input/count.txt
   

   • Specify dimensionality for output in dim.txt, e.g.:

     echo 3 > src/webserver/static/tmp/ASDF/0_input/dim.txt
     

   • Specify mode for PaSiMap in state.txt, e.g.:

     echo unaligned > src/webserver/static/tmp/ASDF/0_input/state.txt
     

     The possible options are unaligned for unaligned protein sequences (in FASTA-format), aligned for MSA of protein sequences (in FASTA-format) and quantifier for pairwise similarities.

   • Specify query in input.txt according to state.txt, e.g. unaligned protein sequences ( in FASTA-format) for unaligned.

     Please refer to Help page of PaSiMap webserver for details.

   • Specify number of datapoints (e.g. sequences) of query in count.txt. For sequences, you can take advantage of the syntax of FASTA-format:

     grep -c '>' src/webserver/static/tmp/ASDF/0_input/input.txt > src/webserver/static/tmp/ASDF/0_input/count.txt
     

3. Activate Virtual Environment for PaSiMap, if not already active:

   # In pasimap directory.
   source venv/bin/activate
   

4. Run job:

   # In pasimap directory.
   ./run_pipeline.sh ASDF