SignalP

Overview

SignalP 6.0 predicts the presence of signal peptides and the location of their cleavage sites in proteins from Archaea, Gram-positive Bacteria, Gram-negative Bacteria and Eukarya. In Bacteria and Archaea, SignalP 6.0 can discriminate between five types of signal peptides:

Sec/SPI: "standard" secretory signal peptides transported by the Sec translocon and cleaved by Signal Peptidase I (Lep)
Sec/SPII: lipoprotein signal peptides transported by the Sec translocon and cleaved by Signal Peptidase II (Lsp)
Tat/SPI: Tat signal peptides transported by the Tat translocon and cleaved by Signal Peptidase I (Lep)
Tat/SPII: Tat lipoprotein signal peptides transported by the Tat translocon and cleaved by Signal Peptidase II (Lsp)
Sec/SPIII: Pilin and pilin-like signal peptides transported by the Sec translocon and cleaved by Signal Peptidase III (PilD/PibD)

Additionally, SignalP 6.0 predicts the regions of signal peptides. Depending on the type, the positions ofn-,h-andc-regionsas well as of other distinctive features are predicted.

SignalP 6.0 is based on a transformer protein language model with a conditional random field for structured prediction.

Using

Use the module name signalp to discover versions available and to load the application.

SignalP’s --mode flag allows for two methods of prediction: fast or slow-sequential. Read more about modes here.

SignalP is installed in two flavors on Beartooth:

A CPU only version specified with -cpu in the module name. Ex: signalp/6.0g-cpu
A GPU version specified with -gpu in the module name. Ex: signalp/6.0g-gpu
- You will need to request a GPU as documented here: Introduction to Job Submission: 02: Memory and GPUs

Getting Help

You may get help by typing signalp -h into the command line for a list of optional arguments.

Multicore

SignalP allows for optimization using the --write_procs, -wp flag. This is the integer number of parallel processes launched for writing output files. This does not allow for multicore processing during prediction, it will only allow for multiple processes when writing the files.

... 
#SBATCH --cpus-per-task=32
... 
module load signalp/<version> 
... 
signalp -ff /fastafile/location/file.fasta --output_dir /output/location/ --mode <fast or slow-sequential> -wp 32
...

GPU Example

If you are using the signalp/6.0g-gpu version you will want to request a gpu node with --gres=gpu:<however many you need>
Below is an example you may use as a basic template to request one gpu on a node:

... 
#SBATCH --gres=gpu:1 
#SBATCH --partition=teton-gpu 
... 
module load signalp/6.0g-gpu
... 
signalp -ff /fastafile/location/file.fasta --output_dir /output/location/ --mode <fast or slow-sequential> 
...