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286534 occurrences (No.87 in the rank) during 5 years in the PubMed. [no cache] 500 found

313) Species- and isochore-specific variations of the matrices and of the positioning motifs are demonstrated.

--- ABSTRACT ---

PMID:24266748 DOI:10.1080/07391102.2013.855143

2015 Journal of biomolecular structure & dynamics

* Visible periodicity of strong nucleosome DNA sequences.

- Fifteen years ago, Lowary and Widom assembled nucleosomes on synthetic random sequence DNA molecules, selected the strongest nucleosomes and discovered that the TA dinucleotides in these strong nucleosome sequences often appear at 10-11 bases from one another or at distances which are multiples of this period. We repeated this experiment computationally, on large ensembles of natural genomic sequences, by selecting the strongest nucleosomes--i.e. those with such distances between like-named dinucleotides, multiples of 10.4 bases, the structural and sequence period of nucleosome DNA. The analysis confirmed the periodicity of TA dinucleotides in the strong nucleosomes, and revealed as well other periodic sequence elements, notably classical AA and TT dinucleotides. The matrices of DNA bendability and their simple linear forms--nucleosome positioning motifs--are calculated from the strong nucleosome DNA sequences. The motifs are in full accord with nucleosome positioning sequences derived earlier, thus confirming that the new technique, indeed, detects strong nucleosomes. Species- and isochore-specific variations of the matrices and of the positioning motifs are demonstrated. The strong nucleosome DNA sequences manifest the highest hitherto nucleosome positioning sequence signals, showing the dinucleotide periodicities in directly observable rather than in hidden form.

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(1)158 that	(10)5 good	(19)3 excellent	(28)2 efficacy
(2)48 the	(11)5 increased	(20)3 more	(29)2 greater
(3)40 a	(12)5 significantly	(21)3 no	(30)2 how
(4)23 by	(13)4 as	(22)3 that,	(31)2 successful
(5)21 to	(14)4 better	(23)2 acceptable	(32)2 through
(6)13 in	(15)4 improved	(24)2 and	(33)2 using
(7)12 null	(16)4 its	(25)2 both
(8)11 an	(17)4 similar	(26)2 decreased
(9)8 for	(18)3 between	(27)2 differential

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--- WordNet output for demonstrated --- Overview of verb demonstrate The verb demonstrate has 4 senses (first 4 from tagged texts) 1. (24) show, demo, exhibit, present, demonstrate -- (give an exhibition of to an interested audience; "She shows her dogs frequently"; "We will demo the new software in Washington") 2. (22) prove, demonstrate, establish, show, shew -- (establish the validity of something, as by an example, explanation or experiment; "The experiment demonstrated the instability of the compound"; "The mathematician showed the validity of the conjecture") 3. (2) attest, certify, manifest, demonstrate, evidence -- (provide evidence for; stand as proof of; show by one's behavior, attitude, or external attributes; "His high fever attested to his illness"; "The buildings in Rome manifest a high level of architectural sophistication"; "This decision demonstrates his sense of fairness") 4. (1) demonstrate, march -- (march in protest; take part in a demonstration; "Thousands demonstrated against globalization during the meeting of the most powerful economic nations in Seattle") Overview of adj demonstrated The adj demonstrated has 1 sense (first 1 from tagged texts) 1. (1) demonstrated -- (having been demonstrated or verified beyond doubt) --- WordNet end ---