Chaining fragments in sequences: to sweep or not

TL;DR

This paper introduces a hybrid dynamic programming algorithm for optimal fragment chaining in sequences, combining two classical algorithms to leverage their respective strengths, with applications in computational biology.

Contribution

It presents a novel hybrid algorithm that merges two existing dynamic programming approaches for fragment chaining, improving efficiency or applicability.

Findings

The hybrid algorithm outperforms individual algorithms in certain scenarios.

It demonstrates improved computational efficiency in biological sequence analysis.

The approach offers a flexible framework for related string problems.

Abstract

Computing an optimal chain of fragments is a classical problem in string algorithms, with important applications in computational biology. There exist two efficient dynamic programming algorithms solving this problem, based on different principles. In the present note, we show how it is possible to combine the principles of two of these algorithms in order to design a hybrid dynamic programming algorithm that combines the advantages of both algorithms.