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

Lily Major, Amanda Clare, Jacqueline W Daykin, Benjamin Mora, Christine Zarges

Abstract read

In one paragraph

Article in Journal of heuristics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

5 authors.

Lily MajorDepartment of Computer Science, Aberystwyth University, Penglais, Aberystwyth, SY23 3DB UK.ORCID 0000-0002-5783-8432

Amanda Clare *Department of Computer Science, Aberystwyth University, Penglais, Aberystwyth, SY23 3DB UK.ORCID 0000-0001-8315-3659

Jacqueline W Daykin *Department of Computer Science, Aberystwyth University, Penglais, Aberystwyth, SY23 3DB UK.ORCID 0000-0003-1123-8703

Benjamin Mora *Computer Science Department, Swansea University, Bay Campus, Fabian Way, Swansea, SA1 8EN UK.ORCID 0000-0002-2945-3519

Christine Zarges *Department of Computer Science, Aberystwyth University, Penglais, Aberystwyth, SY23 3DB UK.ORCID 0000-0002-2829-4296

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The Burrows-Wheeler Transform (BWT) is a string transformation technique widely used in areas such as bioinformatics and file compression. Many applications combine a run-length encoding (RLE) with the BWT in a way which preserves the ability to query the compressed data efficiently. However, these methods may not take full advantage of the compressibility of the BWT as they do not modify the alphabet ordering for the sorting step embedded in computing the BWT. Indeed, any such alteration of the alphabet ordering can have a considerable impact on the output of the BWT, in particular on the number of runs. For an alphabet

Indexed as

Alphabet orderingBurrows–Wheeler transformCompressionLocal searchRandom samplingRun-length encoding

Identifiers

PMID40084382

DOI10.1007/s10732-025-09548-3

PMCPMC11905289

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