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C-InterSecture-a computational tool for interspecies comparison of genome architecture. / Nuriddinov, M.; Fishman, V.

в: Bioinformatics (Oxford, England), Том 35, № 23, 01.12.2019, стр. 4912-4921.

Результаты исследований: Научные публикации в периодических изданияхстатьяРецензирование

Harvard

Nuriddinov, M & Fishman, V 2019, 'C-InterSecture-a computational tool for interspecies comparison of genome architecture', Bioinformatics (Oxford, England), Том. 35, № 23, стр. 4912-4921. https://doi.org/10.1093/bioinformatics/btz415

APA

Vancouver

Nuriddinov M, Fishman V. C-InterSecture-a computational tool for interspecies comparison of genome architecture. Bioinformatics (Oxford, England). 2019 дек. 1;35(23):4912-4921. doi: 10.1093/bioinformatics/btz415

Author

Nuriddinov, M. ; Fishman, V. / C-InterSecture-a computational tool for interspecies comparison of genome architecture. в: Bioinformatics (Oxford, England). 2019 ; Том 35, № 23. стр. 4912-4921.

BibTeX

@article{88f2cfc2f1004c508b4a1508abfd643a,
title = "C-InterSecture-a computational tool for interspecies comparison of genome architecture",
abstract = "MOTIVATION: Recent development of Hi-C technique, a biochemical method to study 3D genome architecture, provided large amount of information describing spatial organization of chromosomes in different cell types and species. While multiple tools are available for analysis and comparison of Hi-C data of different cell types, there are almost no resources for systematic interspecies comparison. RESULTS: To fill this gap, we developed C-InterSecture, a computational pipeline allowing systematic comparison of genome architecture between species. C-InterSecture allows statistical comparison of contact frequencies of individual pairs of loci, as well as interspecies comparison of contacts pattern within defined genomic regions, i.e. topologically associated domains. We employed C-InterSecture to compare mammalian and avian genome organization and showed how evolutionary changes of genomic distance affect 3D architecture of vertebrate's genome. AVAILABILITY AND IMPLEMENTATION: C-InterSecture is implemented as a collection of python scripts freely available on GitHub repository at https://github.com/NuriddinovMA/C-InterSecture. Jucebox-compatible .hic files produced by C-InterSecture are available at http://genedev.bionet.nsc.ru/site/CIntersecture.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.",
keywords = "REVEALS, PRINCIPLES, MAP",
author = "M. Nuriddinov and V. Fishman",
note = "Publisher Copyright: {\textcopyright} 2019 The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.",
year = "2019",
month = dec,
day = "1",
doi = "10.1093/bioinformatics/btz415",
language = "English",
volume = "35",
pages = "4912--4921",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "23",

}

RIS

TY - JOUR

T1 - C-InterSecture-a computational tool for interspecies comparison of genome architecture

AU - Nuriddinov, M.

AU - Fishman, V.

N1 - Publisher Copyright: © 2019 The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.

PY - 2019/12/1

Y1 - 2019/12/1

N2 - MOTIVATION: Recent development of Hi-C technique, a biochemical method to study 3D genome architecture, provided large amount of information describing spatial organization of chromosomes in different cell types and species. While multiple tools are available for analysis and comparison of Hi-C data of different cell types, there are almost no resources for systematic interspecies comparison. RESULTS: To fill this gap, we developed C-InterSecture, a computational pipeline allowing systematic comparison of genome architecture between species. C-InterSecture allows statistical comparison of contact frequencies of individual pairs of loci, as well as interspecies comparison of contacts pattern within defined genomic regions, i.e. topologically associated domains. We employed C-InterSecture to compare mammalian and avian genome organization and showed how evolutionary changes of genomic distance affect 3D architecture of vertebrate's genome. AVAILABILITY AND IMPLEMENTATION: C-InterSecture is implemented as a collection of python scripts freely available on GitHub repository at https://github.com/NuriddinovMA/C-InterSecture. Jucebox-compatible .hic files produced by C-InterSecture are available at http://genedev.bionet.nsc.ru/site/CIntersecture.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

AB - MOTIVATION: Recent development of Hi-C technique, a biochemical method to study 3D genome architecture, provided large amount of information describing spatial organization of chromosomes in different cell types and species. While multiple tools are available for analysis and comparison of Hi-C data of different cell types, there are almost no resources for systematic interspecies comparison. RESULTS: To fill this gap, we developed C-InterSecture, a computational pipeline allowing systematic comparison of genome architecture between species. C-InterSecture allows statistical comparison of contact frequencies of individual pairs of loci, as well as interspecies comparison of contacts pattern within defined genomic regions, i.e. topologically associated domains. We employed C-InterSecture to compare mammalian and avian genome organization and showed how evolutionary changes of genomic distance affect 3D architecture of vertebrate's genome. AVAILABILITY AND IMPLEMENTATION: C-InterSecture is implemented as a collection of python scripts freely available on GitHub repository at https://github.com/NuriddinovMA/C-InterSecture. Jucebox-compatible .hic files produced by C-InterSecture are available at http://genedev.bionet.nsc.ru/site/CIntersecture.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

KW - REVEALS

KW - PRINCIPLES

KW - MAP

UR - http://www.scopus.com/inward/record.url?scp=85076330375&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btz415

DO - 10.1093/bioinformatics/btz415

M3 - Article

C2 - 31116383

AN - SCOPUS:85076330375

VL - 35

SP - 4912

EP - 4921

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 23

ER -

ID: 22999619