Plascad is a computationally efficient tool designed for automated plasmid classification, ARGs annotation and plasmid visualization.
- Plascad workflow
- Requirements
- Installation
- Usage
- Example
- Output files
- Tips for visualization
- Acknowledgement
- Citation
- Contact
Linux, Python >=3.6, biopython, Prodigal >=2.6.3, blast >=2.7.1, hmmer >=3.2.1
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: 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
wget https://github.com/pianpianyouche/plascad/raw/master/plas_cad/example/example.fasta
Plascad -i example.fasta
The final output of Plascad includes four files for the given plasmid sequences:
- Summary file of the plasmid classification results.
- Genetic location of the genes associated with plasmid transfer and antibiotic resistance genes
for both mobilizable and conjugative plasmids. - Html files containing the plasmid maps for all the identified conjugative plasmids.
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
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
example_Conjugative_plasmids_map# folder containing the maps for all the identified conjugative plasmids
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.
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)
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
You CHE, hkucheyou@gmail.com