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What do Eulerian and Hamiltonian cycles have to do with genome assembly?
Many students are taught about genome assembly using the dichotomy between the complexity of finding Eulerian and Hamiltonian cycles (easy versus hard, respectively). This dichotomy is sometimes used to motivate the use of de Bruijn graphs in practice. In this paper, we explain that while de Bruijn...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8136698/ https://www.ncbi.nlm.nih.gov/pubmed/34014915 http://dx.doi.org/10.1371/journal.pcbi.1008928 |
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author | Medvedev, Paul Pop, Mihai |
author_facet | Medvedev, Paul Pop, Mihai |
author_sort | Medvedev, Paul |
collection | PubMed |
description | Many students are taught about genome assembly using the dichotomy between the complexity of finding Eulerian and Hamiltonian cycles (easy versus hard, respectively). This dichotomy is sometimes used to motivate the use of de Bruijn graphs in practice. In this paper, we explain that while de Bruijn graphs have indeed been very useful, the reason has nothing to do with the complexity of the Hamiltonian and Eulerian cycle problems. We give 2 arguments. The first is that a genome reconstruction is never unique and hence an algorithm for finding Eulerian or Hamiltonian cycles is not part of any assembly algorithm used in practice. The second is that even if an arbitrary genome reconstruction was desired, one could do so in linear time in both the Eulerian and Hamiltonian paradigms. |
format | Online Article Text |
id | pubmed-8136698 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-81366982021-06-02 What do Eulerian and Hamiltonian cycles have to do with genome assembly? Medvedev, Paul Pop, Mihai PLoS Comput Biol Education Many students are taught about genome assembly using the dichotomy between the complexity of finding Eulerian and Hamiltonian cycles (easy versus hard, respectively). This dichotomy is sometimes used to motivate the use of de Bruijn graphs in practice. In this paper, we explain that while de Bruijn graphs have indeed been very useful, the reason has nothing to do with the complexity of the Hamiltonian and Eulerian cycle problems. We give 2 arguments. The first is that a genome reconstruction is never unique and hence an algorithm for finding Eulerian or Hamiltonian cycles is not part of any assembly algorithm used in practice. The second is that even if an arbitrary genome reconstruction was desired, one could do so in linear time in both the Eulerian and Hamiltonian paradigms. Public Library of Science 2021-05-20 /pmc/articles/PMC8136698/ /pubmed/34014915 http://dx.doi.org/10.1371/journal.pcbi.1008928 Text en © 2021 Medvedev, Pop https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Education Medvedev, Paul Pop, Mihai What do Eulerian and Hamiltonian cycles have to do with genome assembly? |
title | What do Eulerian and Hamiltonian cycles have to do with genome assembly? |
title_full | What do Eulerian and Hamiltonian cycles have to do with genome assembly? |
title_fullStr | What do Eulerian and Hamiltonian cycles have to do with genome assembly? |
title_full_unstemmed | What do Eulerian and Hamiltonian cycles have to do with genome assembly? |
title_short | What do Eulerian and Hamiltonian cycles have to do with genome assembly? |
title_sort | what do eulerian and hamiltonian cycles have to do with genome assembly? |
topic | Education |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8136698/ https://www.ncbi.nlm.nih.gov/pubmed/34014915 http://dx.doi.org/10.1371/journal.pcbi.1008928 |
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