Analysis of distribution and significance of simple sequence repeats in enteric bacteria Shigella dysenteriae SD197



Batwal Saurabh1, Sitaraman Sneha1, Ranade Suvidya2*, Khandekar Pramod3, Bajaj Shailesh2



1Sinhagad College of Engineering, Wadgaon BK, Pune - 411041; 2Department of chemistry, University of Pune, Maharashtra India; 3Biotechnology Chair, University of Pune


Email; *Corresponding author


Article Type




Received June 13, 2011; Accepted June 28, 2011; Published July 19, 2011



We have explored the possible role of SSR density in genome to generate biological information. In our study, we have checked the SSR (simple sequence repeats) status in virulent and non virulent genes of enteric bacteria to see whether the SSRs distribution contributes to virulence. The genome, plasmid and virulent genes sequences in fasta format were downloaded from NCBI GenBank and VFDB. The sequences were subjected to SSR analysis using software tool ssr.exe. The resulting data was pasted in excel sheet and further analyzed for percentage of each type of SSR. Higher nucleotide repeats have been observed in our study. Overall high density of SSRs can enhance antigenic variance of the pathogen population in a strategy that counteracts the host immune response. Frequency of A and T repeats is higher in the chromosome, plasmid and the virulence genes. However, in dinucleotide repeats the frequencies of GC/CG repeats are higher in genome, whereas plasmid has more of AT/TA repeats. Genome has trinucleotide repeats having predominantly G and C whereas plasmid has trinucleotide repeats having predominantly A and T. The repeat number obtained and percentage of repeats is higher in virulence genes as compared to other gene families. Due to the presence of this large number of SSRs, the organism has an enormous potential for generating this genomic and phenotypic diversity.



Saurabh et al. Bioinformation 6(9): 348-351 (2011)

Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.