A NOVEL ALGORITHM FOR DETECTION OF PALINDROME DNA

Palindromic sequences in DNA are unique genetic configurations where a sequence of nucleotides reads the same forward and backward on complementary strands. In particular, palindrome formation followed by subsequent amplifications are known to cause genetic instability, a hallmark of cancer. Despite the importance of these sequences, detecting palindromic DNA poses significant challenges due to their structural complexity.This paper describes a novel algorithm designed to efficiently detect palindromic sequences, including complex variations that have historically been difficult to identify. The algorithm performs well at identifying imperfect palindromes, palindromes with long arms, and palindromes containing substantial gaps between the arms. These more intricate configurations have been largely overlooked or poorly handled by existing algorithms. Additionally, the algorithm achieves significant speed improvements by optimizing the traditional Smith-Waterman or Needleman-Wunsch algorithms, reducing its complexity from quadratic (<i>O(n</i>^<em>2</em><i>)</i>) to linear (<i>O(nd)</i>, where <i>n</i> is the length of the sequence). The algorithm described here will help the identification and annotation of palindrome sequences and facilitate the research on palindrome sequences and cancer.