Conway-Bromage-Lyndon (CBL): an exact, dynamic representation of k-mer sets.
other · Level V
Where this comes from
- Record sourced from PubMed, PMID 38940123.
- Also identified by DOI 10.1093/bioinformatics/btae217 and PMC identifier 11211824.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
In this article, we introduce the Conway-Bromage-Lyndon (CBL) structure, a compressed, dynamic and exact method for representing k-mer sets. Originating from Conway and Bromage's concept, CBL innovatively employs the smallest cyclic rotations of k-mers, akin to Lyndon words, to leverage lexicographic redundancies. In order to support dynamic operations and set operations, we propose a dynamic bit vector structure that draws a parallel with Elias-Fano's scheme. This structure is encapsulated in a Rust library, demonstrating a balanced blend of construction efficiency, cache locality, and compression. Our findings suggest that CBL outperforms existing dynamic k-mer set methods. Unique to this work, CBL stands out as the only known exact k-mer structure offering in-place set operations. Its different combined abilities position it as a flexible Swiss knife structure for k-mer set management. https://github.com/imartayan/CBL.
Medical subject headings
- Software