CRISPR-Based Salmonella Enterica Serotype Analyzer
CSESA (CRISPR-based Salmonella enterica Serotype Analyzer).
Find the serotype based on the analysis of the new spacers.
Get the new spacers from the molecular sequence and its reverse comple...
Get the new spacer from the molecular sequence.
Get the new spacer from the molecular sequence and map it to the code.
Return the reverse complement of the sequence.
Get the information string from the CSESA s3 object.
Get the CSESA obeject through the two sequence.
Read the three types of input file.
Find the serotype based on the analysis of the new spacers.
Salmonella enterica is a major cause of bacterial food-borne disease worldwide. Serotype identification is the most commonly used typing method to characterize Salmonella isolates. However, experimental serotyping needs great cost on manpower and resources. Recently, we found that the newly incorporated spacer in the clustered regularly interspaced short palindromic repeat (CRISPR) could serve as an effective marker for typing of Salmonella. It was further revealed by Li et. al (2014) <doi:10.1128/JCM.00696-14> that recognized types based on the combination of two newly incorporated spacer in both CRISPR loci showed high accordance with serotypes. Here, we developed an R package 'CSESA' to predict the serotype based on this finding. Considering it’s time saving and of high accuracy, we recommend to predict the serotypes of unknown Salmonella isolates using 'CSESA' before doing the traditional serotyping.