deepsig-biocomp 0.9

DeepSig - Predictor of signal peptides in proteins based on deep learning

DeepSig - Predictor of signal peptides in proteins based on deep learning

Publication

Savojardo C., Martelli P.L., Fariselli P., Casadio R. DeepSig: deep learning improves signal peptide detection in proteins Bioinformatics (2017) 34(10): 1690-1696.

Installation using pip

First, install deepsig-biocomp package using pip:

pip install deepsig-biocomp

Then, clone the deepsig repo from GitHub and export the DEEPSIG_ROOT directory:

git clone [e-mail]:BolognaBiocomp/deepsig.git
cd deepsig
export DEEPSIG_ROOT=$(pwd)

Usage

$ deepsig -h

usage: deepsig.py [-h] -f FASTA -o OUTF -k {euk,gramp,gramn} [-a CPU]

DeepSig: Predictor of signal peptides in proteins

optional arguments:
  -h, --help            show this help message and exit
  -f FASTA, --fasta FASTA
                        The input multi-FASTA file name
  -o OUTF, --outf OUTF  The output tabular file
  -k {euk,gramp,gramn}, --organism {euk,gramp,gramn}
                        The organism the sequences belongs to

The program accepts three mandatory arguments:

• The full path of the input FASTA file containing protein sequences to be predicted;
• The kingdom the sequences belong to. You must specify "euk" for Eukaryotes, "gramp" for Gram-positive bacteria or "gramn" for Gram-negative bacteria;
• The output file where predictions will be stored.

Please, reports bugs to: [e-mail]