التفاصيل البيبلوغرافية
| العنوان: |
Conway–Bromage–Lyndon (CBL): an exact, dynamic representation of k-mer sets. |
| المؤلفون: |
Martayan, Igor, Cazaux, Bastien, Limasset, Antoine, Marchet, Camille |
| المصدر: |
Bioinformatics; 2024 Supplement, Vol. 40, pi48-i57, 10p |
| مصطلحات موضوعية: |
ROTATIONAL motion, KNIVES, LIBRARIES, VOCABULARY |
| مستخلص: |
Summary 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. Availability and implementation https://github.com/imartayan/CBL. [ABSTRACT FROM AUTHOR] |
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