New Error Tolerant Method to Search Long Repeats in Symbol Sequences

TL;DR

This paper introduces a novel error-tolerant method for detecting long repeats in symbol sequences, utilizing a sparse dictionary to enhance speed and accommodate errors, with applications demonstrated in genomics.

Contribution

The paper presents a new gauge-based approach with a sparse dictionary for efficient, error-tolerant detection of long repeats in symbol sequences, improving speed and accuracy.

Findings

Effective identification of long repeats with errors in genomic sequences

Significant acceleration of search process through sparse dictionary

Successful application demonstrated in genomic data analysis

Abstract

A new method to identify all sufficiently long repeating substrings in one or several symbol sequences is proposed. The method is based on a specific gauge applied to symbol sequences that guarantees identification of the repeating substrings. It allows the matching of substrings to contain a given level of errors. The gauge is based on the development of a heavily sparse dictionary of repeats, thus drastically accelerating the search procedure. Some genomic applications illustrate the method. This paper is the extended and detailed version of the presentation at the third International Conference on Algorithms for Computational Biology to be held at Trujillo, Spain, June 21-22, 2016.