About: GenomeLandscaper: Landscape analysis of genome-fingerprints maps assessing chromosome architecture

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An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	GenomeLandscaper: Landscape analysis of genome-fingerprints maps assessing chromosome architecture
Creator	Ai, Hannan Ai, Yuncan Meng, Fanmei
source	PMC
abstract	Assessing correctness of an assembled chromosome architecture is a central challenge. We create a geometric analysis method (called GenomeLandscaper) to conduct landscape analysis of genome-fingerprints maps (GFM), trace large-scale repetitive regions, and assess their impacts on the global architectures of assembled chromosomes. We develop an alignment-free method for phylogenetics analysis. The human Y chromosomes (GRCh.chrY, HuRef.chrY and YH.chrY) are analysed as a proof-of-concept study. We construct a galaxy of genome-fingerprints maps (GGFM) for them, and a landscape compatibility among relatives is observed. But a long sharp straight line on the GGFM breaks such a landscape compatibility, distinguishing GRCh38p1.chrY (and throughout GRCh38p7.chrY) from GRCh37p13.chrY, HuRef.chrY and YH.chrY. We delete a 1.30-Mbp target segment to rescue the landscape compatibility, matching the antecedent GRCh37p13.chrY. We re-locate it into the modelled centromeric and pericentromeric region of GRCh38p10.chrY, matching a gap placeholder of GRCh37p13.chrY. We decompose it into sub-constituents (such as BACs, interspersed repeats, and tandem repeats) and trace their homologues by phylogenetics analysis. We elucidate that most examined tandem repeats are of reasonable quality, but the BAC-sized repeats, 173U1020C (176.46 Kbp) and 5U41068C (205.34 Kbp), are likely over-repeated. These results offer unique insights into the centromeric and pericentromeric regions of the human Y chromosomes.
has issue date	2018-01-18(xsd:dateTime)
bibo:doi	10.1038/s41598-018-19366-2
bibo:pmid	29348569
has license	cc-by
sha1sum (hex)	b72e220b6500d2251e103f23d64b2f96f6e082f2
schema:url	https://doi.org/10.1038/s41598-018-19366-2
resource representing a document's title	GenomeLandscaper: Landscape analysis of genome-fingerprints maps assessing chromosome architecture
has PubMed Central identifier	PMC5773709
has PubMed identifier	29348569
schema:publication	Sci Rep
resource representing a document's body	covid:b72e220b6500d2251e103f23d64b2f96f6e082f2#body_text
is schema:about of	named entity 'maps' named entity 'GFM' named entity 'repeats' named entity 'tandem repeats' named entity 'human' covid:arg/b72e220b6500d2251e103f23d64b2f96f6e082f2 named entity 'construct' named entity 'global' named entity 'analysis' named entity 'phylogenetics' named entity 'conduct' named entity 'homologues' named entity 'chrY' named entity 'autosomal' named entity 'pericentromeric' named entity 'distance matrix' named entity 'human genome' named entity 'phylogenetic tree' named entity 'genomes' named entity 'reference genome' named entity 'Phylip' named entity 'But' named entity 'geometric analysis' named entity 'chrY' named entity 'maps' named entity 'segment' named entity 'chromosome' named entity 'chromosomes' named entity 'Mbp' named entity 'geometric analysis' named entity 'Kbp' named entity 'BACs' named entity 'genome' named entity 'phylogenetics' named entity 'Kbp' named entity 'chrY' named entity 'chromosome architecture' named entity 'genome' named entity 'chromosomes' named entity 'chrY' named entity 'centromere' named entity 'megabase' named entity 'pericentromeric' named entity 'three-dimensional' named entity 'genome' named entity 'reference genome' named entity 'phylogenetics' named entity 'Mbp' named entity 'algorithm' named entity 'phylogenetic tree' named entity 'Mbp' named entity 'phylogenetic network' named entity 'BLAST search' named entity 'algorithm' named entity 'Euclidean distance matrix' named entity 'genome' named entity 'H. sapiens' named entity 'clones' named entity 'Scientific REPORts' named entity 'Kbp' named entity 'alpha satellite' named entity 'chimpanzee' named entity 'linear sequence' named entity 'BACs' named entity 'autosomal' named entity 'chromosomes' named entity 'tandem repeats' named entity 'consensus tree' named entity 'descendents' named entity 'continuous distribution' named entity 'base pairs' named entity 'database' named entity 'genomes' named entity 'primates' named entity 'BACs' named entity 'pericentromeric' named entity 'Kbp' named entity 'phylogenetic' named entity 'tandem repeats'

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