A method to find palindromes in nucleic acid sequences

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.

A reference catalog of DNA palindromes in the human genome and their variations in 1000 Genomes

“…These limitations can be circumvented by employing computational methods to identify palindromic sequences from sequenced genomes. A linear-time algorithm to identify palindromic sequences is available, but it can identify only exact palindromes 2 . A prior study on the distribution of palindromes in the human genome was limited and provided insufficient details about the locations of all palindromes.…”

“…For example, as shown in Fig. 1, the sequence on the positive strand 5′-GACA| TGTC-3′ is a palindrome since GACA is followed by its complement CTGT, but appearing in reverse order as TGTC 2 . When a palindromic sequence is folded at its midpoint, the base pairs (bp) on the two halves are complementary.…”