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Title

Detecting motifs and patterns at mobile genetic element insertion site

 

Authors

Bhuvan Bhaskar Dev1, 2, Aman Malik1 & Kamal Rawal1*

 

Affiliation

1Department of Biotechnology, Jaypee Institute of Information Technology, Noida 201307, UP, India; 2Infosys Ltd, Bangalore, Karnataka, India.

 

Email

kamal.rawal@jiit.ac.in; *Corresponding author

 

Article Type

Hypothesis

 

Date

Received July 17, 2012; Accepted July 23, 2012; Published August 24, 2012

Abstract

Mobile genetic elements (MGEs) occupy major proportion of eukaryotic genomes and are present in significant numbers in prokaryote genomes also. Here we report a new method which extracts a motif at the site of insertion of MGE using tools such as DNA SCANNER. The flanking region of the insertion site is extracted and is analyzed in DNA Scanner for physiochemical properties like protein-interaction measures, energy profiles as well as structural parameters. In case significant signals are observed, the most frequently occurring n-mer (5E. histolytica, signals for EhSine1 are found at around 5 bps upstream of insertion and most frequently occurring motif is found to be AAGGT and TCGAA. Signals for Ty3 element in S. cerevisiae are found at 0-3 bps upstream of tRNA, and most frequent motif is GTTCGA (6 bps), GGTTCGA (7 bps) and GGTTCGAT (8 bps). P-element of Drosophila showed remarkable dyad peaks suggesting palindromic site of insertion.

 

Citation

Dev et al. Bioinformation 8(16): 777-786 (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.