Detecting the homology of DNA-sequences based on the variety of optimal alignments: a case study

TL;DR

This paper introduces a new method for assessing DNA sequence homology by analyzing the diversity of optimal alignments, and compares it with BLAST using four gene examples.

Contribution

It presents a novel approach based on the variety of optimal alignments for DNA homology detection, offering an alternative to traditional methods.

Findings

The new method provides comparable results to BLAST in homology detection.

The approach highlights differences in sequence similarity not captured by conventional methods.

It demonstrates potential for more nuanced DNA sequence analysis.

Abstract

We consider a novel approach of measuring the homology of DNA sequences based of the variety of optimal alignments in the longest common subsequence sense. The proposed approach is compared with BLAST in measuring the homology of four genes.