Installation

Installing PARAS and PARASECT from source

Installation time: ~10 minutes

Install PARAS and PARASECT

conda create -n paras python==3.9
conda activate paras
pip install paras

conda install -c bioconda muscle==3.8.1551
conda install -c bioconda hmmer2
conda install -c bioconda hmmer

Help menus:

paras -h
parasect -h

Standard PARAS run:

paras -i <path_to_your_input.fasta> -o <path_to_your_output_folder>

Standard PARASECT run:

parasect -i <path_to_your_input.fasta> -o <path_to_your_output_folder>

PARAS run with all substrates model:

paras -i <path_to_your_input.fasta> -o <path_to_your_output_folder> -j all_substrates -all_substrates 

PARASECT run using bacterial model:

parasect -i <path_to_your_input.fasta> -o <path_to_your_output_folder> -j bacterial -bacterial

PARAS run with structure-guided feature extraction:

paras -i -i <path_to_your_input.fasta> -o <path_to_your_output_folder> -j structure_extraction -p

PARASECT run with custom SMILES:

parasect -i <path_to_your_input.fasta> -o <path_to_your_output_folder> -exclude_standard_substrates -j custom_smiles -smiles <path_to_your_smiles.tsv>

PARASECT run with structure-guided feature extraction:

parasect -i <path_to_your_input.fasta> -o <path_to_your_output_folder> -j structure_extraction -p