A Markovian genomic concatenation model guided by persymmetric matrices

Hart, Andrew; Sobottka, Marcelo

doi:10.48550/arxiv.1805.02231

Cited by 1 publication

(5 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In particular, the allegation of the S-H model that each chirochore could be approximated for an ℵ-generated matrix should still be properly investigated. The estimations made in [65] were crude and could be improved by using the results obtained in [30]. Furthermore, from [30,Equations (4) and ( 5)], if the hypothesis that each bacterial genome is a particular realization of the S-H for a same matrix L is true, then we should find that the following ratios 1)…”

Section: Final Discussionmentioning

confidence: 99%

“…The estimations made in [65] were crude and could be improved by using the results obtained in [30]. Furthermore, from [30,Equations (4) and ( 5)], if the hypothesis that each bacterial genome is a particular realization of the S-H for a same matrix L is true, then we should find that the following ratios 1)…”

Section: Final Discussionmentioning

confidence: 99%

“…A matrix P satisfying (6) for some L and M with L ij = L α(j)α(i) and M i = M α(i) is said to be an ℵ-generated matrix and a sequence which is a realization of the stationary Markov chain (P, π) is said to be an ℵ-generated sequence. In [30] it was given formulations of the S-H model as a couple of two hidden Markov chains [30, Theorems 1 and 2]. Furthermore, [30,Theorems 4] provided a way to find a matrix L and a vector M that generated a given ℵ-generated matrix P , while [30,Theorems 11 and 12] proved that in a sequence x y − −m≤ ≤n produced by the S-H model we have all the following sequences being ℵ-generated:…”

Section: Conserved Patternsmentioning

confidence: 99%

“…In [30] it was given formulations of the S-H model as a couple of two hidden Markov chains [30, Theorems 1 and 2]. Furthermore, [30,Theorems 4] provided a way to find a matrix L and a vector M that generated a given ℵ-generated matrix P , while [30,Theorems 11 and 12] proved that in a sequence x y − −m≤ ≤n produced by the S-H model we have all the following sequences being ℵ-generated:…”

Section: Conserved Patternsmentioning

confidence: 99%

“…In particular, [30,Theorem 12] proved that sequences presenting ISP are always ℵ-generated. Finally it was proposed two measures to asses how far some given sequence is from being ℵ-generated and what is the matrix L that best fits the given sequence.…”

Section: Conserved Patternsmentioning

confidence: 99%

See 4 more Smart Citations

Intra-strand symmetries and asymmetries in bacterial DNA: Evolutive features or relics of primordial genomes?

Sobottka¹

2022

Preprint

View full text Add to dashboard Cite

In this work we analyze some models used to explain the origins of intra-strand parity and strand compositional asymmetries in bacterial genomes. Due to the particular way that these two features emerge in bacterial DNA, we performed our analysis from the perspective that they are complementary phenomena that should be addressed together. Although most of the models for these features try to explain them as consequence of evolutionary mechanisms, recently it was proposed that they could be 'relics' of some primordial genome that were conserved thorough out the genome evolution. We shall pay special attention to the S-H model, which is, up to the date, the unique model proposed as a possible explanation for intra-strand parity and strand compositional asymmetries in primordial genomes as mere consequence of randomness under chemical/physical constraints. In particular, we shall discuss possible directions to test some of the hypotheses of the S-H model, and we will present a possible formulation of the S-H model as an evolutive model too.

show abstract

Section: Final Discussionmentioning

confidence: 99%