SignalIP-Sapelo2

Category

Bioinformatics

Program On

Sapelo2

Version

4.1f

Author / Distributor

SignalP

Description

"SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes.". More details are at SignalP

Running Program

Also refer to Running Jobs on Sapelo2

For more information on Environment Modules on Sapelo2 please see the Lmod page.

• Version 4.1f, installed in /usr/local/apps/eb/SignalP/4.1f-foss-2016b.

To use this version of SignalP, please first load the module with

ml SignalP/4.1f-foss-2016b

Sample job submission script (sub.sh) to run SignalP in a batch job:

#PBS -S /bin/bash
#PBS -N j_SignalP
#PBS -q batch
#PBS -l nodes=1:ppn=1:AMD
#PBS -l walltime=480:00:00
#PBS -l mem=10gb

cd $PBS_O_WORKDIR
ml SignalP/4.1f-foss-2016b
time signalp [options]

where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of nodes and cores per node, and the job name need to be modified appropriately as well.

Example of job submission

qsub  sub.sh 

Documentation

ml SignalP/4.1f-foss-2016b
signalp -h

  Description: Predict signal peptide and cleavage site.

  Usage: /usr/local/apps/eb/SignalP/4.1f-foss-2016b/signalp -f <format>  -p <graphics-type> -k -s <networks> -t <organism-type> -m <fasta-file> -n <gff-file> -v -l <logfile> -u <value>  -U <value> -w -h -c <value> -T <temp dir> -V <fasta-file(s)>
  Options:
  -f   Setting the output format ('short', 'long', 'summary' or 'all'). Default: 'short'
  -g   Graphics 'png' or 'png+eps'. Default: 'Off'
  -k   Keep temporary directory. Default: 'Off'
  -s   Signal peptide networks to use ('best' or 'notm'). Default: 'best'
  -t   Organism type> (euk, gram+, gram-). Default: 'euk'
  -m   Make fasta file with mature sequence. Default: 'Off'
  -n   Make gff file of processed sequences. Default: 'Off'
  -T   Specify temporary file directory. Default: /usr/local/apps/tmp/SignalP-4.1f-foss-2016b
  -w   web predictions. Default: 'Off'
  -u   user defined D-cutoff for noTM networks
  -U   user defined D-cutoff for TM networks
  -M   Minimal predicted signal peptide length. Default: [10]
  -c   truncate to sequence length - 0 means no truncation. Default '70'
  -l   Logfile if -v is defined. Default: 'STDERR'
  -v   Verbose. Default: 'Off'
  -V   Print SignalP version and exit
  -h   Print this help information

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Installation

source code from SignalP

System

64-bit Linux