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Related Experiment Video

Updated: May 22, 2025

BEST: Barcode Enabled Sequencing of Tetrads

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Heuristics for the run-length encoded Burrows-Wheeler transform alphabet ordering problem.

Lily Major¹, Amanda Clare¹, Jacqueline W Daykin^1,2,3

¹Department of Computer Science, Aberystwyth University, Penglais, Aberystwyth, SY23 3DB UK.

Journal of Heuristics

|March 14, 2025

Summary

This summary is machine-generated.

Optimizing alphabet order for the Burrows-Wheeler Transform (BWT) significantly improves run-length encoding (RLE) compression. A local search strategy effectively finds better orderings than random sampling for enhanced data compressibility.

Keywords:

Alphabet ordering Burrows–Wheeler transform Compression Local search Random sampling Run-length encoding

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Last Updated: May 22, 2025

BEST: Barcode Enabled Sequencing of Tetrads

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Area of Science:

Computational biology
Data compression algorithms
String processing

Background:

The Burrows-Wheeler Transform (BWT) is crucial for bioinformatics and file compression.
Combining BWT with run-length encoding (RLE) allows efficient data querying.
Current methods often overlook alphabet ordering's impact on BWT compressibility.

Purpose of the Study:

To investigate alphabet ordering's effect on run-length encoded BWT (RLBWT) size.
To develop a heuristic approach for finding optimal alphabet orderings.
To improve compression efficiency by modifying the BWT's sorting step.

Main Methods:

Exploration of non-trivial alphabet ordering cases for RLBWT minimization.
Comparison of random sampling versus local search strategies for alphabet ordering.
Analysis of initial orderings like ASCII, letter appearance, and letter frequency.

Main Results:

Random sampling of alphabet orderings typically yields sub-optimal compression.
Local search strategies demonstrate significant compression improvements in few steps.
The choice of alphabet ordering substantially impacts the number of runs in RLBWT.

Conclusions:

Alphabet ordering is a critical, yet often overlooked, factor in BWT compression.
A local search heuristic offers a practical and effective method for optimizing RLBWT.
This research demonstrates achievable gains in compressibility through informed alphabet ordering.