Strong Inhomogeneity in Triplet Distribution Alongside a Genome

Sadovsky, Michael G.; Nikitina, Xenia

doi:10.1007/978-3-319-16480-9_25

Cited by 1 publication

(5 citation statements)

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“…This question is rather acute, since numerous inhomogeneities in this distribution may bring problems in assembling, annotation and further analysis of genetic entities. We explore the generalized approach to reveal some inhomogeneities in the starts distribution similar to [5][6][7][8][9][10][11]. Here a genome is considered as a symbol sequence, and we refrain from implementation of any biological knowledge "till the end"; in other words, we seek for the highly unexpected sites in the symbol sequences and the procedure is free from any biological knowledge.…”

Section: Discussionmentioning

confidence: 99%

“…To reveal the structuredness in the strings containing the nucleotides with various numbers of starts of reads, we used the idea of information capacity (3)(4)(5); this is an averaged measure telling on the distribution character in general, but nothing could be understood on individual level. To enhance the analysis, an idea of information valuable words [5][6][7][8][9][10] could be implemented. The idea is based on the detail analysis of (4) definition: if f ω ≈ f ω , then the corresponding term in the sum ( 4) is close to zero.…”

Section: Discussionmentioning

confidence: 99%

“…Here we follow the second approach that is completely similar to that one used to study the statistical properties of nucleotide sequences [5][6][7][8][9][10][11].…”

Section: Study Of the Real Distribution Of Start Points Of Reads Along A Genomementioning

confidence: 99%

“…where n ω is the number of copies of a word ω, and N is the length of a sequence; to make the definition (2) feasible, one must connect a sequence into a ring, see details in [5][6][7][8][9][10][11]. Such closure results in appearance of q − 1 phantom words in a dictionary, while we neglect them.…”

Section: Simulation Of Start Points Of Reads: Theoretical Backgroundmentioning

confidence: 99%

“…here we derive f (ω q ) from f (ω q−1 ), see details in [5][6][7][8][9][10][11]. Finally, one must compare the real frequency dictionary W q to that one bearing the most expected continuations: W q .…”

Section: Simulation Of Start Points Of Reads: Theoretical Backgroundmentioning

confidence: 99%

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Reads in NGS Are Distributed over a Sequence Very Inhomogeneously

Sadovsky

Kobets

Khodos

et al. 2019

Bioinformatics and Biomedical Engineering

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Distribution of read starts over a sequences genetic entity is studied. Key question was whether the starts are distributed uniformly and homogeneously along a sequence, or there exist some spots of the increased local density of the starts. To answer the question, 15 bacterial genomes have been studied. It was found that some genomes exhibit extremely far distribution pattern, from an homogeneity, while others show lower level of the inhomogeneity. The inhomogeneity level was determined through the Kullback-Leibler distance between the real string distribution, and that one bearing the most probable continuations of the shorter strings.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

“…Here we follow the second approach that is completely similar to that one used to study the statistical properties of nucleotide sequences [5][6][7][8][9][10][11].…”

Section: Study Of the Real Distribution Of Start Points Of Reads Along A Genomementioning

confidence: 99%