Background:
DNA and Protein sequences of an organism contain a variety of repeated
structures of various types. These repeated structures play an important role in Molecular biology as
they are related to genetic backgrounds of inherited diseases. They also serve as a marker for DNA
mapping and DNA fingerprinting. Efficient searching of maximal and super maximal repeats in
DNA/Protein sequences can lead to many other applications in the area of genomics. Moreover, these
repeats can also be used for identification of critical diseases by finding the similarity between
frequency distributions of repeats in viruses and genomes (without using alignment algorithms).
Objective:
The study aims to develop an efficient tool for searching maximal and super maximal repeats
in large DNA/Protein sequences.
Methods:
The proposed tool uses a newly introduced data structure Induced Enhanced Suffix Array
(IESA). IESA is an extension of enhanced suffix array. It uses induced suffix array instead of classical
suffix array. IESA consists of Induced Suffix Array (ISA) and an additional array-Longest
Common Prefix (LCP) array. ISA is an array of all sorted suffixes of the input sequence while LCP
array stores the lengths of the longest common prefixes between all pairs of consecutive suffixes in
an induced suffix array. IESA is known to be efficient w.r.t. both time and space. It facilitates the
use of secondary memory for constructing the large suffix-array.
Results:
An open source standalone tool named MSR-IESA for searching maximal and super maximal
repeats in DNA/Protein sequences is provided at https://github.com/sanjeevalg/MSRIESA. Experimental
results show that the proposed algorithm outperforms other state of the art works w.r.t. to
both time and space.
Conclusion:
The proposed tool MSR-IESA is remarkably efficient for the analysis of DNA/Protein
sequences, having maximal and super maximal repeats of any length. It can be used for identification
of well-known diseases.
