To determine the plasmid sequence type (ST) of an unknown sample using the pMLST (plasmid multilocus sequence typing) tool

To determine the plasmid sequence type (ST) of an unknown sample using the pMLST (plasmid multilocus sequence typing) tool with default parameters, you would typically follow these steps [1-3]:

• Input Data: Prepare the sequence data of the unknown sample in a suitable format. This could be the raw sequencing reads (FASTQ format) or assembled contigs (FASTA format).
• Access the pMLST Tool: Visit the website or server hosting the pMLST tool. pMLST is often hosted by the Center for Genomic Epidemiology (CGE) or other bioinformatics platforms.
• Upload Data: Upload the sequence data of the unknown sample to the pMLST tool. Follow the instructions provided on the website to upload your data files.
• Run Analysis: Initiate the analysis using the default parameters provided by the pMLST tool. This typically involves selecting the appropriate analysis options and specifying the input data files.
• Retrieve Results: After the analysis is complete, retrieve the results from the pMLST tool. The output may include information such as the predicted plasmid ST type, along with any other relevant metadata or annotations.
• Interpret Results: Review the results to determine the plasmid ST type assigned to the unknown sample by the pMLST tool. The plasmid ST type represents a specific combination of alleles at designated loci, which is used for plasmid typing and classification.

It's important to note that the specific steps and user interface may vary depending on the version of the pMLST tool and the hosting platform. Additionally, interpretation of the results should consider any limitations or caveats associated with the analysis method and the quality of the input data.

References:

1. Carattoli, A., Zankari, E., García-Fernández, A., Voldby Larsen, M., Lund, O., Villa, L., Møller Aarestrup, F., & Hasman, H. (2014). In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrobial agents and chemotherapy, 58(7), 3895–3903.

2. https://www.genomicepidemiology.org/

3. https://www.ncbi.nlm.nih.gov/geo/info/seq.html