K-mer natural vector and its application to the phylogenetic analysis of genetic sequences

Wen, Jia; Chan, Raymond H.; Yau, Shek Chung; He, Rong; Yau, Stephen S.-T.

doi:10.1016/j.gene.2014.05.043

Cited by 60 publications

(54 citation statements)

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“…In recent years, many studies have approached the investigation of DNA strings and genomes by means of algorithms, information theory and formal languages 11 12 13 14 15 16 17 18 19 20 21 22 , and methods were developed for investigating whole genome structures. In particular, dictionaries of words occurring in genomes, distributions defined over genomes, and concepts related to word occurrences and frequencies have been very useful and seem to characterize important genomic features relevant in biological contexts 23 24 25 26 27 28 29 30 . Dictionaries are, in essence, finite formal languages.…”

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confidence: 99%

Informational laws of genome structures

Bonnici

Manca

2016

Sci Rep

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In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.

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confidence: 99%

Informational laws of genome structures

Bonnici

Manca

2016

Sci Rep

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“…With the help of the guide tree, StrainSeeker is able to detect the last common ancestor on the sub-species level. For the present work, we used an alignment-free k-mer-based distance method similar to the k-mer natural vector method [11,12] to construct the tree of 2,758 bacterial strains. To test the accuracy of our tree, the E. coli sp.…”

Section: Advantages and Limitations Of Guide Tree-based Strain Detectmentioning

confidence: 99%

“…Building the guide tree. We used k-mer-based alignment-free methods analogous to [11,12] to calculate the pairwise distance K between all pairs of genomes and to create the guide tree. All 2,758 available bacterial genomes from the NCBI RefSeq database (release 65) were used.…”

Section: Multi-locus Sequence Typing Of E Coli Samplesmentioning

confidence: 99%

StrainSeeker: fast identification of bacterial strains from unassembled sequencing reads using user-provided guide trees

Roosaare

Vaher

Kaplinski

et al. 2016

Preprint

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“…Some people tried to use the k-mer frequencies of genome sequences to construct phylogenetic trees, but the results were not satisfactory. In order to get the consistency with the accepted phylogenetic tree, total kmer set had to be screened [34][35][36][37][38]. It is known that the ideal plan is by using the information of genomewide sequence to characterize genome evolution.…”

Section: Introductionmentioning

confidence: 99%

Intrinsic laws of k-mer spectra of genome sequences and evolution mechanism of genomes

Yang

Yun

et al. 2020

Preprint

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Background K-mer spectra of DNA sequences contain important information about sequence composition and sequence evolution. We want to reveal the evolution rules of genome sequences by studying the k-mer spectra of genome sequences. Results The intrinsic laws of k-mer spectra of 920 genome sequences from primate to prokaryote were analyzed. We found that there are two types of evolution selection modes in genome sequences, named as CG Independent Selection and TA Independent Selection. There is a mutual inhibition relationship between CG and TA independent selections. We found that the intensity of CG and TA independent selections correlates closely with genome evolution and G+C content of genome sequences. The living habits of species are related closely to the independent selection modes adopted by species genomes. Consequently, we proposed an evolution mechanism of genomes in which the genome evolution is determined by the intensities of the CG and TA independent selections and the mutual inhibition relationship. Besides, by the evolution mechanism of genomes, we speculated the evolution modes of prokaryotes in mild and extreme environments in the anaerobic age and the evolving process of prokaryotes from anaerobic to aerobic environment on earth as well as the originations of different eukaryotes. Conclusion We found that there are two independent selection modes in genome sequences. The evolution of genome sequence is determined by the two independent selection modes and the mutual inhibition relationship between them.

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K-mer natural vector and its application to the phylogenetic analysis of genetic sequences

Cited by 60 publications

References 50 publications

Informational laws of genome structures

Informational laws of genome structures

StrainSeeker: fast identification of bacterial strains from unassembled sequencing reads using user-provided guide trees

Intrinsic laws of k-mer spectra of genome sequences and evolution mechanism of genomes

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