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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Mary Ann Liebert, Inc., publishers
2021
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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. |
format | Online Article Text |
id | pubmed-8066347 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Mary Ann Liebert, Inc., publishers |
record_format | MEDLINE/PubMed |
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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