CSESA: an R package to predict Salmonella enterica serotype based on newly incorporated spacer pairs of CRISPR

BMC Bioinformatics

Hao Li¹  Lang Yang¹  Yuqi Liu¹  Hongbin Song²  Peng Li²  Shaofu Qiu²  Xia Zhang³ 

[1] Academy of Military Medical Sciences;Center for Disease Control and Prevention of PLA;School of electronics engineering and computer science, Peking University;

关键词: S. enterica;    Serotyping;    CSESA;   

DOI  :  10.1186/s12859-019-2806-5

来源: DOAJ

【 摘 要 】

Abstract Background Salmonella enterica is a major cause of bacterial food-borne disease worldwide. Immunological serotyping is the most commonly used typing method to characterize S. enterica isolates, but is time-consuming and requires expensive reagents. Here, we developed an R package CSESA (CRISPR-based Salmonella enterica Serotype Analyzer) to predict the serotype based on the CRISPR loci of S. enterica. Results CSESA has implemented the CRISPR typing method CLSPT and extended its coverage on diverse S. enterica serotypes. This package takes CRISPR sequences or the genome sequences as input and provides users with the predicted serotypes. CSESA has shown excellent performance with currently available sequences of S. enterica. Conclusions CSESA is a convenient and useful tool for the prediction of S. enterica serotypes. The application of CSESA package can improve the efficiency of serotyping for S. enterica and reduce the burden of manpower resources. CSESA is freely available from CRAN at https://cran.r-project.org/web/packages/CSESA/.

【 授权许可】

Unknown