BACK TO CONTENTS   |    PDF   |    NEXT

Title

Comparison of simple sequence repeats in Staphylococcus strains using in-silico approach 

 

Authors

Sunil Thorat1* & Prashant Thakare2

 

Affiliation

1Institute of Bioresources and Sustainable Development, Imphal 795001, Manipur, India; 2Department of Biotechnology, S.G.B. Amravati University, Amravati 444602, Maharashtra, India.

 

Email

sunilsthorat.ibsd@nic.in; *Corresponding author

 

Article Type

Hypothesis

 

Date

Received November 15, 2012; Accepted November 16, 2012; Published December 08, 2012

 

Abstract

Staphylococci are Gram-positive bacteria which play an important role in infectious disease and are major causes of community-acquired and hospital-acquired infections. Strains of Staphylococcus aureus are reported as genomically and phenotypically highly heterogeneous; hence in-silico based comparison of genomic data on simple sequence repeats may provide valuable information for understanding the pathogenicity and control measures. This study determined the distribution of a specific group of Simple Sequence Repeats (SSRs), in genome sequences of six Staphylococcus strains (Staphylococcus aureus COL, S.aureus MRSA252, S.aureus MSSA476, S.aureus Mu50, S.aureus MW2, S.aureus N315) and plasmid sequences of four Staphylococcus strains (Staphylococcus aureus COL pT181, Staphylococcus aureus MSSA pSAS, Staphylococcus aureus VRSAp, Staphylococcus aureus, Staphylococcus aureus pN315 DNA) downloaded from the GenBank database for identifying abundance, distribution and composition of SSRs. The data obtained in the present study shows that (i) a large number of tandem repeats are distributed throughout the genome and plasmid sequences. (ii) Number of mononucleotide SSRs decreased rapidly with increase in size of repeat unit. (iii) Total frequency of SSRs in plasmid regions is less than genomic regions. (iv) In all investigated strains, ratios of AT/TA repeats are dominating over GC/CG repeats in genomics as well as plasmid sequences, and (v) Dinucleotide combination of AT is dominated in all the six Staphylococcus genome sequences.

 

Citation

Thorat & Thakare, Bioinformation 8(24): 1182-1186 (2012)
 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

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.