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Symmetry observations in long nucleotide sequences: a commentary on the Discovery Note of Qi and Cuticchia

D. R. Forsdyke
2002 Bioinformatics  
The relative quantities of bases in DNA were determined chemically many years before sequencing technologies permitted direct counting of bases.  ...  Apparently unaware of the rich literature on the topic, bioinformaticists are today rediscovering the 'wheels' of Chargaff, Wyatt and other biochemists.  ...  In his brief paper Prabhu (1993) did not distinguish the contributions of base composition and base order by comparing natural sequences with sequences randomized to destroy the natural order of bases  ... 
doi:10.1093/bioinformatics/18.1.215 pmid:11836239 fatcat:ac62o47x6fh2rodisvvol3rfc4

The global intrinsic curvature of archaeal and eubacterial genomes is mostly contained in their dinucleotide composition and is probably not an adaptation

E. Merino
2000 Nucleic Acids Research  
Until now, the genomic DNA of all eubacteria analyzed has been hyper-curved, its global intrinsic curvature being higher than that of a random sequence.  ...  We also found that, contrary to the predictions of model (ii), the dinucleotide compositions of bacterial genomes were not statistically special in their curvature-related properties (when compared to  ...  Evolution of artificial genomes Evolution of random sequences for increased curvature was as follows. The process started with a 50 000 nt long random sequence.  ... 
doi:10.1093/nar/28.12.2431 pmid:10871377 pmcid:PMC102725 fatcat:si7sbqoafnh5jdqh5vqd6zlv3e

Are mutagenic non D-loop direct repeat motifs in mitochondrial DNA under a negative selection pressure?

Lakshmi Narayanan Lakshmanan, Jan Gruber, Barry Halliwell, Rudiyanto Gunawan
2015 Nucleic Acids Research  
By comparing DR counts in human mtDNA with those in selectively randomized sequences, we also showed that the number of DRs in human mtDNA is primarily determined by global mtDNA properties, such as the  ...  Non D-loop direct repeats (DRs) in mitochondrial DNA (mtDNA) have been commonly implicated in the mutagenesis of mtDNA deletions associated with neuromuscular disease and ageing.  ...  The frequency of DRs in DNA sequences has been shown to increase with bias in nucleotide composition (14) .  ... 
doi:10.1093/nar/gkv299 pmid:25855815 pmcid:PMC4417187 fatcat:u644a6tqxrf5nplqmfkow7jfoi

Mid-Range Inhomogeneity of Eukaryotic Genomes

Larisa Fedorova, Alexei Fedorov
2011 The Scientific World Journal  
This dark DNA has a profound nonrandomness in its sequence composition seen at different scales, from a few nucleotides to regions that span over hundreds of thousands of nucleotides.  ...  These regions are associated with unusual DNA conformations and/or particular DNA properties.  ...  This random sequence is used further for comparison with the natural one.  ... 
doi:10.1100/tsw.2011.82 pmid:21479353 pmcid:PMC5720003 fatcat:rrnpwn2wuveg5etwaewpiv6btq

Compositional segmentation and long-range fractal correlations in DNA sequences

Pedro Bernaola-Galván, Ramón Román-Roldán, José L. Oliver
1996 Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics  
A segmentation algorithm based on the Jensen-Shannon entropic divergence is used to decompose longrange correlated DNA sequences into statistically significant, compositionally homogeneous patches.  ...  Both types of random sequences displayed the same correlation scaling exponents as the original DNA sequence, thus demonstrating that neither the internal structure of patches nor the order in which these  ...  In simple, not long-range correlated DNA sequences, such as those predominantly integrated by coding regions, compositional patches can simply be identified by eye ͑see, for example, ͓9͔͒.  ... 
doi:10.1103/physreve.53.5181 pmid:9964850 fatcat:adekqmbbpbheniuzk3hdltmao4

Ligation of random oligomers leads to emergence of autocatalytic sequence network [article]

Patrick W. Kudella, Alexei V. Tkachenko, Sergei Maslov, Dieter Braun
2020 arXiv   pre-print
Here, we show how nontrivial sequence patterns emerge in a system of random 12mer DNA sequences subject to enzyme-based templated ligation reaction and temperature cycling.  ...  Even without selection for function, the base pairing of DNA with ligation showed a dynamics resembling Darwinian evolution.  ...  The random pool resulted in a similar behavior to the network one but with significantly lower overall concentration of long chains.  ... 
arXiv:2008.07823v1 fatcat:tcrokgrwmba6jkmzwyemziy52e

Distinctive Sequence Features in Protein Coding Genic Non-coding, and Intergenic Human DNA

Roderic Guigó, James W. Fickett
1995 Journal of Molecular Biology  
It appears, thus, that the performance of gene-finding algorithms should be improved by carefully distinguishing the effects of protein coding function from those of mere base compositional variation on  ...  Strong differences in behavior of a number of such statistics are also observed, however when the randomly selected clone sequences are compared with only the non-coding fraction of the genic sequences  ...  Thus, intergenic DNA seems to be characterized by the relative absence of long ORFs, when compared with other classes of DNA.  ... 
doi:10.1006/jmbi.1995.0535 pmid:7473716 fatcat:weltgu6lwrdubh3mjszczmbpz4

Neutralism versus selectionism: Chargaff's second parity rule, revisited

Donald R. Forsdyke
2021 Genetica  
Of Chargaff's four "rules" on DNA base frequencies, the functional interpretation of his second parity rule (PR2) is the most contentious.  ...  Evidence for a local within-species recombination-initiating role of base order was obtained with a novel technology that masked the contribution of base composition to nucleic acid folding energy.  ...  with base substitution rates within one strand of DNA, and the type 2 parity rule (PR2) is concerned with the base composition at equilibrium within one strand of DNA."  ... 
doi:10.1007/s10709-021-00119-5 pmid:33880685 pmcid:PMC8057000 fatcat:3h4ise2wkjhrzdgzwhae3wsja4

Intramolecular base composition heterogeneity of human DNA

Douglas L. Vizard, Frank P. Rinehart, Carol M. Rubin, Carl W. Schmid
1977 Nucleic Acids Research  
DNA sequences having an average length of less than 2000 base pairs are found to be heterogeneous in base composition. These heterogeneous sequences occupy a minimum of 67 to 81% of the human genome.  ...  The intramolecular base composition heterogeneity of human DNA has been investigated by electron microscopic obseirvations of partially denatured structures and by equilibrium solution thermal denaturation  ...  long single copy DNA sequences.5'6 Among those organisms tested, the Drosophila sequence organization is the exception and the more prevalent DNA sequence organization is that typified by Xenopus.4 It  ... 
doi:10.1093/nar/4.11.3753 pmid:593884 pmcid:PMC343198 fatcat:25vvnfs7vnaazlai2i2fx4tynq

Structured sequences emerge from random pool when replicated by templated ligation

Patrick W Kudella, Alexei V Tkachenko, Annalena Salditt, Sergei Maslov, Dieter Braun
2021 Proceedings of the National Academy of Sciences of the United States of America  
Surprisingly, we found the robust creation of long, highly structured sequences with low entropy. At the ligation site, complementary and alternating sequence patterns developed.  ...  The findings showed that replication by random templated ligation from a random sequence input will lead to a highly structured, long, and nonrandom sequence pool.  ...  for their help with the library preparation and the sequencing of the samples.  ... 
doi:10.1073/pnas.2018830118 pmid:33593911 fatcat:3fros22e7fbtffmp6nv23jwxgq

DNA Sequence Correlations Shape Nonspecific Transcription Factor-DNA Binding Affinity

Itamar Sela, David B. Lukatsky
2011 Biophysical Journal  
binding, as compared with poorly occupied regions.  ...  The predicted effect also imposes an upper bound on the size of TF-DNA binding motifs.  ...  We thank Noa Musa-Lempel for help in compiling yeast genomic sequences. D.B.L. acknowledges financial support from Israel Science Foundation grant 1014/09.  ... 
doi:10.1016/j.bpj.2011.04.037 pmid:21723826 pmcid:PMC3127192 fatcat:wa3ccoyu4zbtbd2yzggldhnhoe

Evolution from Primitive Life to Homo sapiens Based on Visible Genome Structures: The Amino Acid World

Kenji Sorimachi
2009 Natural Science  
On the other hand, by graphical presentation of the ratios of the numbers of amino acids present to the total numbers of amino acids presumed from the target gene(s) or genome or those of the numbers of  ...  It is not too much to say that molecular biology, including genome research, has progressed based on the determination of nucleotide or amino acid sequences.  ...  In this analysis, 17 amino acid residues were chosen at random from the amino acid pool based on the complete genome to compare the amino acid composition with those calculated from gene assemblies on  ... 
doi:10.4236/ns.2009.12013 fatcat:yap2cdwdzfa4jnicmqi6e6cd4i

Ligation of random oligomers leads to emergence of autocatalytic sequence network [article]

Patrick W Kudella, Alexei V Tkachenko, Sergei Maslov, Dieter Braun
2020 bioRxiv   pre-print
Here, we show how nontrivial sequence patterns emerge in a system of random 12mer DNA sequences subject to enzyme-based templated ligation reaction and temperature cycling.  ...  Even without selection for function, the base pairing of DNA with ligation showed a dynamics resembling Darwinian evolution.  ...  The random pool resulted 362 in a similar behavior to the network one but with significantly lower overall concentration of long 363 chains.  ... 
doi:10.1101/2020.08.18.253963 fatcat:zb7zqaydxnhj5c524qmigzjl7y

Individual sequences in large sets of gene sequences may be distinguished efficiently by combinations of shared sub-sequences

Mark J Gibbs, John S Armstrong, Adrian J Gibbs
2005 BMC Bioinformatics  
Most current DNA diagnostic tests for identifying organisms use specific oligonucleotide probes that are complementary in sequence to, and hence only hybridize with the DNA of one target species.  ...  The sizes of minimal sub-sequence sets depended mostly on sequence diversity and sub-sequence length and interactions between these parameters.  ...  The Australian Research Council funded a small part of MJG's work on this project. We thank Roger Brown of the Australian National University for suggesting the use of a greedy algorithm.  ... 
doi:10.1186/1471-2105-6-90 pmid:15817134 pmcid:PMC1090557 fatcat:g5sa2bk6tjh4heukbag7prgnxi

General Designs Reveal a Purine-Pyrimidine Structural Code in Human DNA

Dana Cohen
2022 Mathematics  
It reveals that the RY property of a sequence is most distant from randomness in the human genome with respect to the genomic signatures. This is true across all human chromosomes.  ...  The human genome carries a vast amount of information within its DNA sequences.  ...  However, instead of comparing two real genomic DNA sequences, a real sequence is compared with its random equivalent, since the theoretical odds ratio value for the random sequence is 1.0.  ... 
doi:10.3390/math10152723 fatcat:zn7nnglsabdk7fz6xw5q27jmji
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