alexa In Silico Mining of Simple Sequence Repeats in Whole Genome of Xanthomonas sp.
ISSN: 0974-7230

Journal of Computer Science & Systems Biology
Open Access

Like us on:
OMICS International organises 3000+ Global Conferenceseries Events every year across USA, Europe & Asia with support from 1000 more scientific Societies and Publishes 700+ Open Access Journals which contains over 50000 eminent personalities, reputed scientists as editorial board members.

Open Access Journals gaining more Readers and Citations

700 Journals and 15,000,000 Readers Each Journal is getting 25,000+ Readers

This Readership is 10 times more when compared to other Subscription Journals (Source: Google Analytics)

Research Article

In Silico Mining of Simple Sequence Repeats in Whole Genome of Xanthomonas sp.

Mukti Jaiswal and Anjana Pandey*

Nanotechnology and Molecular Biology laboratory, Department of Biotechnology, University of Allahabad, Allahabad-211002, Uttar Pradesh, India

*Corresponding Author:
Anjana Pandey
Department of Biotechnology
University of Allahabad, Allahabad -211002
Uttar Pradesh, India
Tel: +91-9453029719
E-mail: [email protected]

Received Date: July 14, 2014; Accepted Date: August 18, 2014; Published Date: August 20, 2014

Citation: Jaiswal M, Pandey A (2014) In Silico Mining of Simple Sequence Repeats in Whole Genome of Xanthomonas sp. J Comput Sci Syst Biol 7:203-208. doi: 10.4172/jcsb.1000157

Copyright: © 2014 Jaiswal M, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.



In current scenario, microsatellites are a large source of genetic markers. In this study, we mined simple sequence repeats in whole genome of Xanthomonas species (Xanthomonas axonopodis pv. citri, Xanthomonas oryzae pv. oryzae, Xanthomonas campestris pv. Campestris) by in silico methods. A total of 640 SSRs, 377 SSRs and 541 SSRs were detected in whole genome having density of 1SSR/8.08 kb, 1SSR/13.10 kb and 1SSR/9.510 kb for 5175.554 kb, 4941.439 kb and 5148.708 kb sequences length respectively. The results elucidated, only 32 types (0.618%), 39 types (0.789%) and 96 types (1.864%) of SSR sequences were present in Xanthomonas axonopodis pv. citri, Xanthomonas oryzae pv.oryzae and Xanthomonas campestris pv. campestis respectively. Depending on the repeat units, the length of SSRs ranged from 10 to 18 bp for di-, 12 to 27 bp for tri-, 12 to 24 bp for tetra-, 20 to 35 bp for penta-, 24 to 72 for hexa-, 21 to 133 bp for hepta-, 24 to 40 bp for octa- and 27 to 36 bp for nano nucleotide repeats. Di-nucleotide repeats were the most frequent repeat type (70.97%) followed by tri-nucleotide (22.23%), hepta–nucleotide (2.86%), hexa-nucleotide (1.91%) and tetra-nucleotide (1.392%) in all three species of Xanthomonas. Annotation of sequences containing SSRs were also carried out to assign function to each of the sequences. SSR containing sequences of Xanthomonas species could not assign any specific class of protein (77.56%) due to the absence of homologs in the protein sequence database and these could be treated as an ideal molecular marker.


Share This Page

Additional Info

Loading Please wait..
Peer Reviewed Journals
Make the best use of Scientific Research and information from our 700 + peer reviewed, Open Access Journals
International Conferences 2017-18
Meet Inspiring Speakers and Experts at our 3000+ Global Annual Meetings

Contact Us

Agri, Food, Aqua and Veterinary Science Journals

Dr. Krish

[email protected]

1-702-714-7001 Extn: 9040

Clinical and Biochemistry Journals

Datta A

[email protected]

1-702-714-7001Extn: 9037

Business & Management Journals


[email protected]

1-702-714-7001Extn: 9042

Chemical Engineering and Chemistry Journals

Gabriel Shaw

[email protected]

1-702-714-7001 Extn: 9040

Earth & Environmental Sciences

Katie Wilson

[email protected]

1-702-714-7001Extn: 9042

Engineering Journals

James Franklin

[email protected]

1-702-714-7001Extn: 9042

General Science and Health care Journals

Andrea Jason

[email protected]

1-702-714-7001Extn: 9043

Genetics and Molecular Biology Journals

Anna Melissa

[email protected]

1-702-714-7001 Extn: 9006

Immunology & Microbiology Journals

David Gorantl

[email protected]

1-702-714-7001Extn: 9014

Informatics Journals

Stephanie Skinner

[email protected]

1-702-714-7001Extn: 9039

Material Sciences Journals

Rachle Green

[email protected]

1-702-714-7001Extn: 9039

Mathematics and Physics Journals

Jim Willison

[email protected]

1-702-714-7001 Extn: 9042

Medical Journals

Nimmi Anna

[email protected]

1-702-714-7001 Extn: 9038

Neuroscience & Psychology Journals

Nathan T

[email protected]

1-702-714-7001Extn: 9041

Pharmaceutical Sciences Journals

John Behannon

[email protected]

1-702-714-7001Extn: 9007

Social & Political Science Journals

Steve Harry

[email protected]

1-702-714-7001 Extn: 9042

© 2008-2017 OMICS International - Open Access Publisher. Best viewed in Mozilla Firefox | Google Chrome | Above IE 7.0 version