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Zimin patterns in genomes.

Nikol Chantzi1,2, Ioannis Mouratidis1,2, Ilias Georgakopoulos-Soares1,2

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Summary
This summary is machine-generated.

Zimin avoidmers, k-mers without Zimin words, are found in the human genome, particularly in coding regions. These patterns show unique properties and vary across different organisms.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Zimin words are defined as patterns with identical prefixes and suffixes.
  • Sufficiently large strings are expected to contain Zimin words.
  • The presence and properties of k-mers avoiding Zimin words (Zimin avoidmers) in genomes remain largely unexplored.

Purpose of the Study:

  • To investigate the occurrence and characteristics of Zimin avoidmers in the human genome.
  • To analyze the distribution and genomic localization of Zimin avoidmers.
  • To compare Zimin avoidmer patterns across diverse model organisms.

Main Methods:

  • Analysis of k-mer patterns in the human reference genome.
  • Identification and characterization of Zimin avoidmers.
  • Comparative genomics across eight model organisms from bacteria, archaea, and eukaryotes.

Main Results:

  • All k-mers longer than 104 base pairs in the human genome contain Zimin words.
  • Zimin avoidmers are enriched in human coding and Satellite 1 regions.
  • These avoidmers exhibit lower germline insertion/deletion rates.
  • Genomic density and localization of Zimin avoidmers vary significantly across species, with prokaryotes showing higher levels and eukaryotes lower.
  • The longest observed Zimin avoidmer length was 115 base pairs in S. cerevisiae.

Conclusions:

  • Zimin avoidmers exhibit non-uniform distributions within organismal genomes.
  • They possess distinct genomic properties, including reduced mutation rates.
  • Zimin avoidmers disappear at shorter lengths than theoretically predicted across studied genomes.