Speeding Hirschberg Algorithm for Sequence Alignment

TL;DR

This paper improves the Hirschberg algorithm for sequence alignment by significantly reducing its time overhead, making it more efficient while maintaining linear space complexity.

Contribution

It introduces a novel technique that minimizes the temporal cost of the Hirschberg algorithm, enhancing its practicality for sequence alignment tasks.

Findings

Reduced the time overhead of the Hirschberg algorithm to negligible levels

Maintained linear space complexity in sequence alignment

Enhanced efficiency of sequence alignment algorithms

Abstract

The use of Hirschberg algorithm reduces the spatial cost of recovering the Longest Common Subsequence to linear space. The same technique can be applied to similar problems like Sequence Alignment. However, the price to pay is a duplication of temporal cost. We present here a technique to reduce this time overhead to a negligible amount.