Plascad

Plascad is a computationally efficient tool designed for automated plasmid classification, ARGs annotation and plasmid visualization.

Contents

• Plascad workflow
• Requirements
• Installation
• Usage
• Example
• Output files
• Tips for visualization
• Acknowledgement
• Citation
• Contact

Plascad workflow

Plascad first predicts ORFs in the query plasmid sequences and then detects the homologs of genes associated with plasmid transfer by hmmsearch with the built HMM protein profiles. Then, it identifies ARGs by searching against the structed ARGs database (SARGs), at last, a plasmid visualization component using AngularJS is integrated into this pipeline for the visualization of the classified conjugative plasmids.

Requirements

Linux, Python >=3.6, biopython, Prodigal >=2.6.3, blast >=2.7.1, hmmer >=3.2.1

Installation

Plascad can be installed either through conda or pip, though we advise to use Conda.

1, Conda

Use miniconda or anaconda to install Plascad

conda create -n Plascad -y -c bioconda -c pianpianyouche plascad

conda activate Plascad

2, pip3

If you have the dependencies (Python >=3.6, blast >=2.7.1, prodigal >=2.6.3, hmmer >=3.2.1) in your PATH, you can install with pip3

pip3 install Plascad

Usage

Usage: Plascad [-h] [-i] [-n] [-cMOBB CMOBB] [-cMOBC CMOBC] [-cMOBF CMOBF] [-cMOBT CMOBT] [-cMOBPB CMOBPB] [-cMOBH CMOBH] [-cMOBP CMOBP] [-cMOBV CMOBV] [-cMOBQ CMOBQ]

Help:
-h, Show this help message and exit
-i, FASTA file of plasmid sequences -n, Prodigal normal mode, default (meta) -cMOB[B,C,F,T,PB,H,P,V,Q], alignment coverage for MOB HMM profiles

Example

wget https://github.com/pianpianyouche/plascad/raw/master/plas_cad/example/example.fasta

Plascad -i example.fasta

Output files

The final output of Plascad includes four files for the given plasmid sequences:

1. Summary file of the plasmid classification results.
2. Genetic location of the genes associated with plasmid transfer and antibiotic resistance genes
   for both mobilizable and conjugative plasmids.
3. Html files containing the plasmid maps for all the identified conjugative plasmids.

Output of the example fasta file

1. example_plasmids_classification_sum.txt # sumary of the plasmid classification results

Name	plasmid type	ARGs
AJ627386.1	Conj	chloramphenicol__catA;tetracycline__tetB;tetracycline__tetC;tetracycline__tetD;beta-lactam__TEM-1
NC_002377.1	Conj
NC_002483.1	Conj
NC_005014.1	Conj	tetracycline__tetD;tetracycline__tetC;tetracycline__tetB;aminoglycoside__aph(3'')-I;aminoglycoside__aph(6)-I

#note: ARGs are displayed as type_subtype

2. example_Conj_plasmids_loc_sum.txt # Genetic location of the genes associated with transfer and the detected ARGs

Name	Marker genes	c-value & e-value	Genetic location	strand
AJ627386.1	MPFG_41	1.2e-88	35289-35918	1
AJ627386.1	MPFG_44	9.9e-53	38227-38634	1
AJ627386.1	MPFG_51	8.1e-147	44998-46998	-1
AJ627386.1	MPFG_52	9e-123	47013-47954	-1
AJ627386.1	MPFG_ATPase	3.8e-178	38650-41520	1
AJ627386.1	MPFG_T4CP_1	4.4e-193	30481-32730	1
AJ627386.1	MOBH	3.9e-67	55497-57404	1
AJ627386.1	chloramphenicol__catA	1.94e-164	17570-18211	-1
AJ627386.1	tetracycline__tetB	0.0	22897-24102	1
AJ627386.1	tetracycline__tetC	2.36e-166	24215-24883	-1
AJ627386.1	tetracycline__tetD	1.18e-100	24896-25312	1
AJ627386.1	beta-lactam__TEM-1	0.0	50985-51845	-1
NC_002377.1	MPFT_ATPase	1.2e-276	152657-155026	1
NC_002377.1	MPFT_T4CP_1	6.9e-155	170649-172619	1
NC_002377.1	MPFT_virB3	1.6e-29	152331-152657	1
NC_002377.1	MPFT_virB6	4.7e-55	155800-156687	1
NC_002377.1	MPFT_virB8	1.7e-76	156815-157588	1
NC_002377.1	MPFT_virB9	6.3e-97	157585-158466	1
NC_002377.1	MOBQ	5.7e-104	30831-34133	1

#note: c-value for hmmsearch, e-value for blastp

3. example_Conjugative_plasmids_map # folder containing the maps for all the identified conjugative plasmids

Tips for visualization

A plasmid visualization component using AngularJS is integrated into our pipeline, all the plasmid maps are in HTML formats. In order to view the map locally, you need to download the js folder in addtion to the HTML files.

Acknowledgement

If you publish scientific articles using Plascad, please cite the following articles:

Altschul, SF. et al., Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).

Hyatt, D. et al., Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).

Eddy, SR. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).

Yin, XL., ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes. Bioinformatics. 34, 2263-2270 (2018).

Chawdry, R. angularplasmid. (https://github.com/vixis/angularplasmid) (2014)

Citation

If you use Plascad in your work, please cite:

Y. CHE, et al., Conjugative plasmids interact with insertion sequences to shape the horizontal transfer of antimicrobial resistance genes. PNAS. 118(6):e2008731118. doi: 10.1073/pnas.2008731118

Contact

You CHE, [email protected]