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Large-scale Oscillation of Structure-Related DNA Sequence Features in Human Chromosome 21

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Wentian Li, Pedro Miramontes

Genomics · Submitted 14 Jun 2006

abstract compiled · 2026-09-23 · no language-model review

The authors' main claim The following quantities are shown to oscillate with the same 500kb periodicity in human chromosome 21: binding energy calculated by two sets of dinucleotide-based thermodynamic parameters, AA/TT and AAA/TTT bi-/tri-nucleotide density, 5'-TA-3' dinucleotide density, and signal for 10/11-base periodicity of AA/TT or AAA/TTT.

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arXiv IDq-bio/0606016 (version 1)
Pith ID7FM4CGCF, Pith's permanent record of this paper and its review
CitationPedro Miramontes, Wentian Li. "Large-scale Oscillation of Structure-Related DNA Sequence Features in Human Chromosome 21." arXiv:q-bio/0606016 (2006). https://pith.science/paper/7FM4CGCF
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The paper's own sentences, arranged. Each label is drawn from a closed vocabulary; the number beside it is the probability the classifier gave that label. Numbers in the tables are the authors', checked by code. No sentence in this record was written by a model.

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Compiled by classifier-1.13.0 via TypeSafe API, question bank abstract-p1-20260923, 2026-09-23: 1 request, 3,884 input tokens.

What the abstract itself states, as probabilities: claims first 0.10 · states limitation 0.08 · human participants 0.06 · controlled comparison 0.03 · randomized assignment 0.01 · states quantitative result 0.95 · compares with prior results 0.34 · mentions code or data availability 0.02.

The abstract, sentence by sentence

arXiv listing abstract v1. Results and the main claim are underlined; .

Human chromosome 21 is the only chromosome in human genome that exhibits oscillation of (G+C)-content of cycle length of hundreds kilobases (500 kb near the right telomere). We aim at establishing the existence of similar periodicity in structure-related sequence features in order to relate this (G+C)% oscillation to other biological phenomena. The following quantities are shown to oscillate with the same 500kb periodicity in human chromosome 21: binding energy calculated by two sets of dinucleotide-based thermodynamic parameters, AA/TT and AAA/TTT bi-/tri-nucleotide density, 5'-TA-3' dinucleotide density, and signal for 10/11-base periodicity of AA/TT or AAA/TTT. These intrinsic quantities are related to structural features of the double helix of DNA molecules, such as base-pair binding, untwisting/unwinding, stiffness, and a putative tendency for nucleosome formation.

background contribution method result interpretation main claim

What the classifier reports for each sentence. The number is the probability it gave the label.
#sentencerolethe authors' own workstates the main conclusionstrength
s0 Human chromosome 21 is the only chromosome in human genome that exhibits oscillation of (G+C)-content of cycle length of hundreds kilobases (500 kb near the right telomere). background 0.94 0.21 0.14 asserted 1.00
s1 We aim at establishing the existence of similar periodicity in structure-related sequence features in order to relate this (G+C)% oscillation to other biological phenomena. contribution 0.45 0.21 0.04 unclear 0.70
s2 The following quantities are shown to oscillate with the same 500kb periodicity in human chromosome 21: binding energy calculated by two sets of dinucleotide-based thermodynamic parameters, AA/TT and AAA/TTT bi-/tri-nucleotide density, 5'-TA-3' dinucleotide density, and signal for 10/11-base periodicity of AA/TT or AAA/TTT. result 1.00 0.92 0.74 asserted 1.00
s3 These intrinsic quantities are related to structural features of the double helix of DNA molecules, such as base-pair binding, untwisting/unwinding, stiffness, and a putative tendency for nucleosome formation. interpretation 0.98 0.55 0.17 asserted 0.89

What kind of paper the classifier reports this is: empirical study 0.96 · evidence from analysis of existing data 0.76.

What was examined, and what was not

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  • full text
  • figures and tables
  • references and citing sentences
  • relations to other papers
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  • P abstract
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  • T body sentences
  • C citations
  • R cross-paper relations

Every quoted sentence on this record is the authors'. Every label is from Pith's closed vocabulary, with the probability shown beside it. Every number in the measurements table is the authors', checked by code. Record as JSON

The paper
Original abstract

Human chromosome 21 is the only chromosome in human genome that exhibits oscillation of (G+C)-content of cycle length of hundreds kilobases (500 kb near the right telomere). We aim at establishing the existence of similar periodicity in structure-related sequence features in order to relate this (G+C)% oscillation to other biological phenomena. The following quantities are shown to oscillate with the same 500kb periodicity in human chromosome 21: binding energy calculated by two sets of dinucleotide-based thermodynamic parameters, AA/TT and AAA/TTT bi-/tri-nucleotide density, 5'-TA-3' dinucleotide density, and signal for 10/11-base periodicity of AA/TT or AAA/TTT. These intrinsic quantities are related to structural features of the double helix of DNA molecules, such as base-pair binding, untwisting/unwinding, stiffness, and a putative tendency for nucleosome formation.

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