Abstract
Whole genome sequencing (WGS) of bacteria has become a routine method in diagnostic laboratories. One of the most exciting advantages of WGS is the ability to predict antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in a variety of bacteria, which may allow comprehensive investigations of genetic features but also serve for epidemiological studies. A plethora of softwares have been developed for the detailed annotation of DNA sequences, such as RAST (Rapid Annotation using Subsystem Technology), Resfinder, ISfinder, INTEGRALL and The Transposon Registry. Unfortunately, up to now, a reliable annotation tool of the combination of ARGs and MGEs is not available to researchers, and the generation of genbank files requires much manual input. Here, we present a new webserver which allows the annotation of ARGs, ISs, integron, and transposable elements at the same time. The algorithm generates genbank files automatically, which are compatible with easyfig for comparative genomic analysis.
Key Points
There exist a number of software for DNA sequence annotation, RAST (Rapid Annotation using Subsystem Technology), Resfinder, ISfinder, INTEGRALL and The Transposon Registry.
A reliable annotation tool of the combination of ARGs and MGEs is not available to researchers, and the generation of genbank files requires much manual input.
We present a new webserver which allows the annotation of ARGs, ISs, integron, and transposable elements at the same time. The algorithm generates genbank files automatically, which are compatible with easyfig for comparative genomic analysis.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Note:
Xiaoting Hua is an associate professor of the Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University. His research interests are on the mechanism of bacterial resistance and evolution.
Qian Liang graduated from the Department of Mathematics, Beijing Jiaotong University. She is a bioinformatics researcher fellow in the Zhejiang Institute of Microbiology, and mainly research about whole genome sequence typing of important pathogens.
Jintao He is an MSc student of the Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University. His research interest is on the resistance mechanism of Acinetoabcter baumannii.
Meixia Wang received the B.S. and M.S. degrees from college of Chemistry and Chemical Engineering, Lanzhou University, China in 2011 and 2014, respectively. Now, she is currently working at Zhejiang Institute of Microbiology. His focuses on the research on the field of genome sequencing analysis.
Wenjie Hong graduated from Hunan University in 2017, now is engaged in microbial research in Zhejiang Institute of Microbiology. He is concerned about microbiomics analysis and machine learning.
Jun Wu graduated with a master’s degree from the College of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, China in 2019. He is currently the deputy director of the Center for Disease Control and Prevention of Lin’an District, Hangzhou, mainly engaged in pathogenic microorganism research.
Bian Lu received her B.S. degree from College of laboratory medicine, Wenzhou Medical University, China in 2011. Now, she is a department director in Xiaoshan Center for Disease Control and Prevention, Hangzhou. Her research is mainly about molecular biology of bacteria and clinical microbiological trial.
Sebastian Leptihn is an associate professor at the Edinburgh Institute of Zhejiang University. His group is investigating bacterial membrane insertion & assembly and function of membrane proteins, while also exploring medical and technological aspects of bacteriophages, including phage therapy.
Yunsong Yu is a professor of the Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University. He focuses on the research on the surveillance of bacterial resistance, the mechanism of bacterial resistance and the treatment of the infections caused by multi-resistant bacteria.
Huan Chen received his PhD from College of Life Sciences, Zhejiang University, China in 2008. Now, he is a professor in Zhejiang Institute of Microbiology. His research is mainly about whole genome sequence typing of important pathogens.
