BACK TO CONTENTS   |    PDF   |    PREVIOUS   |    NEXT

Title

A method to find palindromes in nucleic acid sequences

 

Authors

Ramnath Anjana$, Mani Shankar$, Marthandan Kirti Vaishnavi & Kanagaraj Sekar*

 

Affiliation

Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560012, India.

 

Email

sekar@physics.iisc.ernet.in; *Corresponding author

 

Article Type

Hypothesis

 

Date

Received December 01, 2012; Revised February 08, 2013; Accepted February 11, 2013; Published March 02, 2013

 

Abstract

Various types of sequences in the human genome are known to play important roles in different aspects of genomic functioning. Among these sequences, palindromic nucleic acid sequences are one such type that have been studied in detail and found to influence a wide variety of genomic characteristics. For a nucleotide sequence to be considered as a palindrome, its complementary strand must read the same in the opposite direction. For example, both the strands i.e the strand going from 5 to 3 and its complementary strand from 3 to 5 must be complementary. A typical nucleotide palindromic sequence would be TATA (5 to 3) and its complimentary sequence from 3 to 5 would be ATAT. Thus, a new method has been developed using dynamic programming to fetch the palindromic nucleic acid sequences. The new method uses less memory and thereby it increases the overall speed and efficiency. The proposed method has been tested using the bacterial (3891 KB bases) and human chromosomal sequences (Chr-18: 74366 kb and Chr-Y: 25554 kb) and the computation time for finding the palindromic sequences is in milli seconds.

 

Keywords

Palindrome, Genome, Complimentarity, Even-numbered.

 

Citation

Anjana et al.  Bioinformation 9(5): 255-258 (2013)

 

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.