Large scale multi-species palindrome study using distributed in-memory computing

Palindromic DNA has many interesting and functional properties, including the ability to form non-canonical DNA structures such as hairpins, cruciforms, and slipped strand structures. Palindromes also serve important roles in binding sites and enzyme activity, and have a strong effect on mutation rates. Palindromes are abundant in most genomes, often occurring within coding sequences, though in many instances it is still not clear how their presence affects genomic functions. The identification and study of palindromic DNA is essential to the progression of our understanding of the genome. To address this need, we present a novel method using an in-memory computing environment for identifying, extracting, and indexing palindromes in a searchable database for all mammals in Ensembl release 80. We discuss the preliminary results of a multi-species study on palindromic DNA, focusing on the size, frequency, and distribution of palindromes. Utilizing a Big Data ecosystem enables us to generate the largest palindrome database to date, comprising 42 genomes. Our study offers new insight into the dynamics of palindromes and facilitates future investigation.