FLR: A Revolutionary Alignment-Free Similarity Analysis Methodology for DNA-Sequences.

Belal Medhat, Ahmed Shawish

IEEE/ACM transactions on computational biology and bioinformatics 2021 Sep-Oct

filter terms:

algorithms (4)

analysis sequences (3)

dna sequences (2)

humans (1)

research (1)

sequence analysis, dna (1)

Sizes of these terms reflect their relevance to your search.

This paper introduces a novel alignment-free sequence analysis methodology. Its main idea is based on introducing a new representation of the DNA-Sequence. This representation breaks the dependency between the DNA bases that exist in the traditional string presentation. We called it the Four-Lists-Representation (FLR). Based on the FLR, a series of revolutionary algorithms for searching, map-discovery, similarity-score analysis, and similarity-visualization have been developed. They are combined in what we call the FLR Methodology. The paper also studies most of the available similarity analysis techniques in a comprehensive state-of-art review. The conducted extensive simulation and theoretical studies confirm the outperformance of the whole set of FLR-based algorithms in terms of speed and memory consumption in comparison to a long list of available similarity analysis algorithms. The ability to provide a similarity-map, similarity-score, and similarity-graph as a set of evidence-based rationales makes the quality of results provided by the proposed methodology presents a new edge in this field and promises a new area of genome-based research.

Citation

Belal Medhat, Ahmed Shawish. FLR: A Revolutionary Alignment-Free Similarity Analysis Methodology for DNA-Sequences. IEEE/ACM transactions on computational biology and bioinformatics. 2021 Sep-Oct;18(5):1924-1936