About: Extending Maximal Perfect Haplotype Blocks to the Realm of Pangenomics

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About: Extending Maximal Perfect Haplotype Blocks to the Realm of Pangenomics Goto Sponge NotDistinct Permalink

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Extending Maximal Perfect Haplotype Blocks to the Realm of Pangenomics
Creator	Mumey, Brendan Williams, Lucia
Source	PMC
abstract	Recent work provides the first method to measure the relative fitness of genomic variants within a population that scales to large numbers of genomes. A key component of the computation involves finding conserved haplotype blocks, which can be done in linear time. Here, we extend the notion of conserved haplotype blocks to pangenomes, which can store more complex variation than a single reference genome. We define a maximal perfect pangenome haplotype block and give a linear-time, suffix tree based approach to find all such blocks from a set of pangenome haplotypes. We demonstrate the method by applying it to a pangenome built from yeast strains.
has issue date	2020-02-01(xsd:dateTime)
bibo:doi	10.1007/978-3-030-42266-0_4
has license	no-cc
sha1sum (hex)	780fa8499fed33aa3c5ed60f1877f016fab71825
schema:url	https://doi.org/10.1007/978-3-030-42266-0_4
resource representing a document's title	Extending Maximal Perfect Haplotype Blocks to the Realm of Pangenomics
has PubMed Central identifier	PMC7197059
schema:publication	Algorithms for Computational Biology
resource representing a document's body	covid:780fa8499fed33aa3c5ed60f1877f016fab71825#body_text
is schema:about of	named entity 'pangenome' named entity 'Perfect' named entity 'Haplotype' named entity 'LINEAR' named entity 'LARGE' named entity 'COMPUTATION' named entity 'APPROACH' named entity 'CONSERVED' named entity 'GENOMIC' named entity 'REFERENCE GENOME' named entity 'perfect' named entity 'strains' named entity 'blocks' named entity 'pangenomes' named entity 'haplotype' named entity 'relative fitness' named entity 'genomes' named entity 'linear sequence' named entity 'pangenome' named entity 'nucleotides' named entity 'SNPs' named entity 'graph' named entity 'SNPs' named entity 'SNP' named entity 'linear time' named entity 'yeast' named entity 'data set' named entity 'genetic variants' named entity 'data set' named entity 'SNP' named entity 'internal nodes' named entity 'genetic variants' named entity 'graph' named entity 'graph' named entity 'suffix tree' named entity 'population genetics' named entity 'nucleotides' named entity 'haplotype block' named entity 'De Bruijn' named entity 'algorithm' named entity 'suffix tree' named entity 'haplotype' named entity 'yeast' named entity 'SNP' named entity 'reference sequence' named entity 'nucleotide' named entity 'SNPs' named entity 'Burrows-Wheeler' named entity 'pangenome' named entity 'haplotype' named entity 'evolution' named entity 'chromosome' named entity 'pangenome' named entity 'sequence data' named entity 'n + 1' named entity 'SNP' named entity 'SNP' named entity 'suffix tree' named entity 'suffix tree' named entity 'haplotypes' named entity 'haplotype' named entity 'SNP' named entity 'reference case' named entity 'yeast' named entity 'maximum-likelihood' named entity 'introgressed' named entity 'SNPs' named entity 'suffix tree' named entity 'SNP' named entity 'graph' named entity 'haplotype block' named entity 'haplotype block' named entity 'graph' named entity 'chromosome' named entity 'O(1) time' named entity 'k-mers' named entity 'sequenced genome' named entity 'yeast' named entity 'pangenome' named entity 'relative fitness' named entity 'linear time' named entity 'pangenome'

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