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SignalP Peptide Prediction Integration

SignalP Peptide Prediction Integration#

Our program integrates peptide prediction functionality using SignalP. To enable this feature, please follow these steps:

  1. Activate SignalP in your program by setting the parameter use_signalP=True.

  2. Acquire an academic license for SignalP and download it from the official site.

  3. Extract the perl file from the downloaded tarball (signalp-4.1g.Linux.tar.gz) and move it to /usr/bin/signalp.

To run the program with SignalP, use the following command:

run_dbcan EscheriaColiK12MG1655.fna prok --out_dir output_EscheriaColiK12MG1655 --use_signalP=TRUE

Warning

If you lack permission to access /usr/bin, specify the path of the SignalP executable file using the -sp or --signalP_path parameter. Here’s an example command:

run_dbcan EscheriaColiK12MG1655.fna prok --out_dir output_EscheriaColiK12MG1655 --use_signalP=TRUE -sp /home/lehuang/Downloads/signalp-4.1/signalp

SignalP-4.1 Installation Instructions#

Begin by decompressing the SignalP tarball and navigating to its directory:

tar -xvf signalp-4.1g.Linux.tar.gz && cd signalp-4.1

Inside the signalp-4.1 directory, you’ll find the following files and directories:

(base) lehuang@lehuang:~/Downloads/signalp-4.1$ ls
bin  lib  signalp  signalp.1  signalp-4.1.readme  syn  test

The signalp file is the perl script that will be utilized in your program.

Customizing the SignalP Script#

Modify the “GENERAL SETTINGS, CUSTOMIZE …” section at the start of the signalp file. Ensure these mandatory variables are correctly set:

  • SIGNALP: Specify the full path to the signalp-4.1 directory on your system.

  • outputDir: Choose a directory for storing temporary files (must be writable by all users).

  • MAX_ALLOWED_ENTRIES: Define the maximum number of input sequences allowed per run.

Here’s an example of how to configure these settings in the signalp file:

##############################################################################
#               GENERAL SETTINGS: CUSTOMIZE TO YOUR SITE
##############################################################################

# Full path to the signalp-4.1 directory (mandatory)
BEGIN {
    $ENV{SIGNALP} = '/home/lehuang/Downloads/signalp-4.1';
}

# Directory for temporary files (writable by all users)
my $outputDir = "/home/lehuang/Downloads/signalp-4.1/output";

# Max number of sequences per run (flexible)
my $MAX_ALLOWED_ENTRIES=100000;

Copying the SignalP Script to /usr/bin (if accessible)#

If you have the necessary permissions, use these commands to copy the signalp script:

sudo cp signalp /usr/bin/signalp
sudo chmod 755 /usr/bin/signalp
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