plasmidhunter 1.3

No project description provided

presented by Institute of Food Safety and Health, Illinois Institute of Technology

PlasmidHunter: Accurate and Fast Plasmid Prediction Based on Gene Content Using Machine Learning

Plasmids are extrachromosomal DNA found in microorganisms. They often carry beneficial genes that help bacteria adapt to harsh conditions. Plasmids are also important tools in genetic engineering, gene therapy, and drug production. However, it can be difficult to identify plasmid sequences from chromosomal sequences in genomic and metagenomic data. Here, we have developed a new tool called PlasmidHunter, which uses machine learning to predict plasmid sequences based on gene content profile. PlasmidHunter achieved high accuracies (up to 97.6%) and high speeds in benchmark tests including both simulated contigs and real metagenomic plasmidome data, outperforming other existing tools.

Keywords: artificial intelligence (AI), machine learning (ML), plasmid prediction, genomic sequencing

Installation and run

conda create -n plasmidhunter -c bioconda -y python=3.10 diamond=2.1.8 prodigal

conda activate plasmidhunter

pip install plasmidhunter

plasmidhunter -h

Result Interpretation

The result is a tab-delimited table showing the prediction of each sequence. The columns include Prediction (0: chromosome, 1: plasmid), Probability of 0 (chromosome), and Probability of 1 (plasmid).

Citation

PlasmidHunter: Accurate and fast prediction of plasmid sequences using gene content profile and machine learning

Renmao Tian, Jizhong Zhou, Behzad Imanian

bioRxiv 2023.02.01.526640; doi: https://doi.org/10.1101/2023.02.01.526640

Contact

If you have any questions, please contact Renmao Tian (tianrenmao[at]gmail.com) or Behzad Imanian (bimanian[at]iit.edu).

License

Educational Community License, Version 2.0