SignalP 6.0h-foss-2022b-fast

There is a newer install of SignalP

The SignalP 5.0 tool 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 5.0 can discriminate between three types of signal peptides Sec/SPI (standard signal peptide), Sec/SPII (lipoprotein signal peptide) and Tat/SPI (tat signal peptide). SignalP 5.0 is based on a deep convolutional and recurrent neural network architecture including a conditional random field.

Accessing SignalP 6.0h-foss-2022b-fast

To load the module for SignalP 6.0h-foss-2022b-fast please use this command on the BEAR systems (BlueBEAR and BEAR Cloud VMs):

📋 module load bear-apps/2022b
module load SignalP/6.0h-foss-2022b-fast

BEAR Apps Version

2022b

Architectures

EL8-cascadelake — EL8-icelake — EL8-sapphirerapids

The listed architectures consist of two part: OS-CPU. The OS used is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.

Using Models

The SignalP pytorch model isn't stored in the application directory but in $BB_APPS_DATA/SignalP/models

To specify this alternative directory or any directory of your choosing, pass the --model_dir option to your command string.

For example: signalp6 --fastafile /path/to/input.fasta --organism other --output_dir path/to/be/saved --format txt --mode fast --model_dir "$BB_APPS_DATA/SignalP/models"

You can install additional models of your choosing by following the instructions here and specifying them with the method described above.

More Information

For more information visit the SignalP website.

Dependencies

This version of SignalP has a direct dependency on: foss/2022b matplotlib/3.7.0-gfbf-2022b Python/3.10.8-GCCcore-12.2.0 PyTorch/1.13.1-foss-2022b SciPy-bundle/2023.02-gfbf-2022b tqdm/4.64.1-GCCcore-12.2.0

Other Versions

These versions of SignalP are available on the BEAR systems (BlueBEAR and BEAR Cloud VMs). These will be retained in accordance with our Applications Support and Retention Policy.

Last modified on 17th November 2023