A method to predict clustered repeats in Salmonella genomes / 基础医学与临床

ABSTRACT

Objective To develop a simple method identifying and illustrating clustered repeats in bacterial ge-nomes, and to observe the patterns of clustered repeats in Salmonella genomes.Methods Bacterial genomes were cut to be overlapped pieces of identical size with a sliding window strategy .Each piece of genome fragment was aligned against itself with BLAT integrated in PipMaker , which was further used to build collinearity figures . Collinearity figures were analyzed to identify the clustered repeats.Results With the new pipeline CRpred ( Clustered Repeat Predicter) , Salmonella typhimurium LT2 genome was screened, and in 151 clustered repeats were disclosed.Pattern analysis on these repeats indicated that there were five categories, including low-copy simple tandem repeats, high-copy simple tandem repeats, interspaced tandem repeats, reverse-complementary re-peats, and interspaced reverse-complementary repeats.Nine repeat regions in LT2 genome were discovered which could not be simply classified into the 5 categories defined above.Conclusions A new, simple and intuitive strategy is proposed to identify and show clustered repeats in genomes , providing clues for CRISPR , VNTR and oth-er repeat-related studies .