SMM-system: A mining tool to identify specific markers in Salmonella enterica.
This report presents SMM-system, a software package that implements various personalized pre- and post-BLASTN tasks for mining specific markers of microbial pathogens. The main functionalities of SMM-system are summarized as follows: (i) converting multi-FASTA file, (ii) cutting interesting genomic sequence, (iii) automatic high-throughput BLASTN searches, and (iv) screening target sequences. The utility of SMM-system was demonstrated by using it to identify 214 Salmonella enterica-specific protein-coding sequences (CDSs). Eighteen primer pairs were designed based on eighteen S. enterica-specific CDSs, respectively. Seven of these primer pairs were validated with PCR assay, which showed 100% inclusivity for the 101 S. enterica genomes and 100% exclusivity of 30 non-S. enterica genomes. Three specific primer pairs were chosen to develop a multiplex PCR assay, which generated specific amplicons with a size of 180bp (SC1286), 238bp (SC1598) and 405bp (SC4361), respectively. This study demonstrates that SMM-system is a high-throughput specific marker generation tool that can be used to identify genus-, species-, serogroup- and even serovar-specific DNA sequences of microbial pathogens, which has a potential to be applied in food industries, diagnostics and taxonomic studies. SMM-system is freely available and can be downloaded from http://foodsafety.sjtu.edu.cn/SMM-system.html.
Joint Sino-US Food Safety Research Center and Bor Luh Food Safety Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China.
Shuijing
S
Yu
Weibing
W
Liu
Chunlei
C
Shi
Dapeng
D
Wang
Xianlong
X
Dan
Xiao
X
Li
Xianming
X
Shi
D019295:Computational Biology / Q000379:methods*; D017931:DNA Primers / Q000235:genetics; D005798:Genes, Bacterial; D005819:Genetic Markers; D005827:Genetics, Microbial / Q000379:methods*; D016133:Polymerase Chain Reaction; D019779:Salmonella enterica / Q000235:genetics*; D017385:Sequence Homology
D017931:DNA Primers; D005819:Genetic Markers