A method to find palindromes in nucleic acid sequences.

Ramnath Anjana,Marthandan Kirti Vaishnavi,Mani Shankar,Kanagaraj Sekar

doi:10.6026/97320630009255

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.

Highlights

A palindrome, in the literary sense, refers to a word or a phrase that reads the same in both directions, i.e when it is read in forward and reverse
For a nucleotide sequence to be considered as a palindrome, its complementary strand must read the same in the opposite direction [2]
Case Study 1 The efficiency of the proposed method is tested by using the genome of the bacterium Bacillus amyloliquefaciens which contains 3,918,589 bases and is 3.8MB in size

Summary

Introduction

A palindrome, in the literary sense, refers to a word or a phrase that reads the same in both directions, i.e when it is read in forward and reverse. The importance of detecting such inverted repeats in both protein as well as nucleotide sequences and the methods used for the same has been elucidated before [5,6,7]. The proposed method locates all palindromic sequences that are present in a given nucleotide based on queries given by the user. The first choice given by number 1 indicates that the user requires a palindromic sequence greater than or equal to a certain length.

Results

Conclusion