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Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length

Universal hitting sets (UHS) are sets of words that are unavoidable: every long enough sequence is hit by the set (i.e., it contains a word from the set). There is a tight relationship between UHS and minimizer schemes, where minimizer schemes with low density (i.e., efficient schemes) correspond to...

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Autores principales: Zheng, Hongyu, Kingsford, Carl, Marçais, Guillaume
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Mary Ann Liebert, Inc., publishers 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8066347/
https://www.ncbi.nlm.nih.gov/pubmed/33325773
http://dx.doi.org/10.1089/cmb.2020.0432
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author Zheng, Hongyu
Kingsford, Carl
Marçais, Guillaume
author_facet Zheng, Hongyu
Kingsford, Carl
Marçais, Guillaume
author_sort Zheng, Hongyu
collection PubMed
description Universal hitting sets (UHS) are sets of words that are unavoidable: every long enough sequence is hit by the set (i.e., it contains a word from the set). There is a tight relationship between UHS and minimizer schemes, where minimizer schemes with low density (i.e., efficient schemes) correspond to UHS of small size. Local schemes are a generalization of minimizer schemes that can be used as replacement for minimizer scheme with the possibility of being much more efficient. We establish the link between efficient local schemes and the minimum length of a string that must be hit by a UHS. We give bounds for the remaining path length of the Mykkeltveit UHS. In addition, we create a local scheme with the lowest known density that is only a log factor away from the theoretical lower bound.
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spelling pubmed-80663472021-04-26 Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length Zheng, Hongyu Kingsford, Carl Marçais, Guillaume J Comput Biol Research Articles Universal hitting sets (UHS) are sets of words that are unavoidable: every long enough sequence is hit by the set (i.e., it contains a word from the set). There is a tight relationship between UHS and minimizer schemes, where minimizer schemes with low density (i.e., efficient schemes) correspond to UHS of small size. Local schemes are a generalization of minimizer schemes that can be used as replacement for minimizer scheme with the possibility of being much more efficient. We establish the link between efficient local schemes and the minimum length of a string that must be hit by a UHS. We give bounds for the remaining path length of the Mykkeltveit UHS. In addition, we create a local scheme with the lowest known density that is only a log factor away from the theoretical lower bound. Mary Ann Liebert, Inc., publishers 2021-04-01 2021-04-20 /pmc/articles/PMC8066347/ /pubmed/33325773 http://dx.doi.org/10.1089/cmb.2020.0432 Text en © Hongyu Zheng, et al., 2020. Published by Mary Ann Liebert, Inc. https://creativecommons.org/licenses/by/4.0/This Open Access article is distributed under the terms of the Creative Commons License (http://creativecommons.org/licenses/by/4.0 (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
spellingShingle Research Articles
Zheng, Hongyu
Kingsford, Carl
Marçais, Guillaume
Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length
title Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length
title_full Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length
title_fullStr Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length
title_full_unstemmed Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length
title_short Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length
title_sort lower density selection schemes via small universal hitting sets with short remaining path length
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8066347/
https://www.ncbi.nlm.nih.gov/pubmed/33325773
http://dx.doi.org/10.1089/cmb.2020.0432
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