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Minimal Absent Words in Four Human Genome Assemblies

Minimal absent words have been computed in genomes of organisms from all domains of life. Here, we aim to contribute to the catalogue of human genomic variation by investigating the variation in number and content of minimal absent words within a species, using four human genome assemblies. We compa...

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Autores principales: Garcia, Sara P., Pinho, Armando J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3248429/
https://www.ncbi.nlm.nih.gov/pubmed/22220210
http://dx.doi.org/10.1371/journal.pone.0029344
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author Garcia, Sara P.
Pinho, Armando J.
author_facet Garcia, Sara P.
Pinho, Armando J.
author_sort Garcia, Sara P.
collection PubMed
description Minimal absent words have been computed in genomes of organisms from all domains of life. Here, we aim to contribute to the catalogue of human genomic variation by investigating the variation in number and content of minimal absent words within a species, using four human genome assemblies. We compare the reference human genome GRCh37 assembly, the HuRef assembly of the genome of Craig Venter, the NA12878 assembly from cell line GM12878, and the YH assembly of the genome of a Han Chinese individual. We find the variation in number and content of minimal absent words between assemblies more significant for large and very large minimal absent words, where the biases of sequencing and assembly methodologies become more pronounced. Moreover, we find generally greater similarity between the human genome assemblies sequenced with capillary-based technologies (GRCh37 and HuRef) than between the human genome assemblies sequenced with massively parallel technologies (NA12878 and YH). Finally, as expected, we find the overall variation in number and content of minimal absent words within a species to be generally smaller than the variation between species.
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spelling pubmed-32484292012-01-04 Minimal Absent Words in Four Human Genome Assemblies Garcia, Sara P. Pinho, Armando J. PLoS One Research Article Minimal absent words have been computed in genomes of organisms from all domains of life. Here, we aim to contribute to the catalogue of human genomic variation by investigating the variation in number and content of minimal absent words within a species, using four human genome assemblies. We compare the reference human genome GRCh37 assembly, the HuRef assembly of the genome of Craig Venter, the NA12878 assembly from cell line GM12878, and the YH assembly of the genome of a Han Chinese individual. We find the variation in number and content of minimal absent words between assemblies more significant for large and very large minimal absent words, where the biases of sequencing and assembly methodologies become more pronounced. Moreover, we find generally greater similarity between the human genome assemblies sequenced with capillary-based technologies (GRCh37 and HuRef) than between the human genome assemblies sequenced with massively parallel technologies (NA12878 and YH). Finally, as expected, we find the overall variation in number and content of minimal absent words within a species to be generally smaller than the variation between species. Public Library of Science 2011-12-29 /pmc/articles/PMC3248429/ /pubmed/22220210 http://dx.doi.org/10.1371/journal.pone.0029344 Text en Garcia, Pinho. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Garcia, Sara P.
Pinho, Armando J.
Minimal Absent Words in Four Human Genome Assemblies
title Minimal Absent Words in Four Human Genome Assemblies
title_full Minimal Absent Words in Four Human Genome Assemblies
title_fullStr Minimal Absent Words in Four Human Genome Assemblies
title_full_unstemmed Minimal Absent Words in Four Human Genome Assemblies
title_short Minimal Absent Words in Four Human Genome Assemblies
title_sort minimal absent words in four human genome assemblies
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3248429/
https://www.ncbi.nlm.nih.gov/pubmed/22220210
http://dx.doi.org/10.1371/journal.pone.0029344
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