Determining the minimum functional length of k-mers: Evidence for the 7-mer threshold from yeast genome

IF 0.9 Q4 GENETICS & HEREDITY

Gene Reports Pub Date : 2025-08-05 DOI:10.1016/j.genrep.2025.102309

Deliang Zhou , Jianli Liu , Wen Jin

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Abstract

k-mers play an important role in the function and evolution of DNA sequences and should have a minimum functional length. Based on the analysis of (1) all core and linker DNA in yeast, and (2) all gene and intergenic sequences in yeast, the minimum functional length of k-mers was determined using the log-ratio of relative frequency. The following conclusions were obtained:

(1)
7-mers represent the minimum functional length of the basic functional fragments of DNA sequences, while k-mers with k < 7 constitute the basic component fragments of DNA sequences;
(2)
7-mers are the minimum length k-mers that drive DNA sequences to produce sequence function and evolution;
(3)
7-mers are the minimum length k-mers that drive the separation of function and evolution among different types of sequences.

These conclusions represent major theoretical breakthroughs and have significant implications: (1) They support the conclusion from Reference 24 that the minimum functional length of k-mers is 7, fully affirming the accuracy and reliability of this minimum functional length; (2) They elucidate the roles and characteristics of functional and component fragments of DNA sequences, revealing the driving force behind the generation and separation of DNA sequence function and evolution.

Abstract Image

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确定k-mers的最小功能长度：酵母基因组7-mer阈值的证据

k-mers在DNA序列的功能和进化中起着重要作用，应该具有最小的功能长度。通过对酵母中所有核心DNA和连接子DNA，以及酵母中所有基因和基因间序列的分析，利用相对频率对数比确定了k-mers的最小功能长度。得到以下结论：(1)7-mers代表DNA序列基本功能片段的最小功能长度，而k-mers具有k <；(2)7-mers是驱动DNA序列产生序列功能和进化的最小长度k-mers；(3)7-mers是驱动不同类型序列之间功能分离和进化的最小长度k-mers。这些结论是重大的理论突破，具有重要意义：(1)支持文献24中k-mers最小功能长度为7的结论，充分肯定了该最小功能长度的准确性和可靠性；(2)阐明了DNA序列的功能片段和组成片段的作用和特征，揭示了DNA序列功能产生、分离和进化的驱动力。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Gene Reports Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

3.30

自引率

7.70%

发文量

246

审稿时长

49 days

期刊介绍： Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.