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A relative Lempel–Ziv complexity: Application to comparing biological sequences

One of the main tasks in biological sequence analysis is biological sequence comparison. Numerous efficient methods have been developed for sequence comparison. Traditional sequence comparison is based on sequence alignment. In this report, we propose a novel alignment-free method based on the relat...

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Detalles Bibliográficos
Autores principales: Liu, Liwei, Li, Dongbo, Bai, Fenglan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier B.V. 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7094452/
https://www.ncbi.nlm.nih.gov/pubmed/32226089
http://dx.doi.org/10.1016/j.cplett.2012.01.061
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author Liu, Liwei
Li, Dongbo
Bai, Fenglan
author_facet Liu, Liwei
Li, Dongbo
Bai, Fenglan
author_sort Liu, Liwei
collection PubMed
description One of the main tasks in biological sequence analysis is biological sequence comparison. Numerous efficient methods have been developed for sequence comparison. Traditional sequence comparison is based on sequence alignment. In this report, we propose a novel alignment-free method based on the relative Lempel–Ziv complexity to compare biological sequences. The vertebrate transferring genomes and the spike protein sequences are prepared and tested to evaluate the validity of the method. We use this method to build phylogenetic tree of two groups of the sequences. The result demonstrates that our method is powerful and efficient.
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spelling pubmed-70944522020-03-25 A relative Lempel–Ziv complexity: Application to comparing biological sequences Liu, Liwei Li, Dongbo Bai, Fenglan Chem Phys Lett Article One of the main tasks in biological sequence analysis is biological sequence comparison. Numerous efficient methods have been developed for sequence comparison. Traditional sequence comparison is based on sequence alignment. In this report, we propose a novel alignment-free method based on the relative Lempel–Ziv complexity to compare biological sequences. The vertebrate transferring genomes and the spike protein sequences are prepared and tested to evaluate the validity of the method. We use this method to build phylogenetic tree of two groups of the sequences. The result demonstrates that our method is powerful and efficient. Elsevier B.V. 2012-03-19 2012-02-01 /pmc/articles/PMC7094452/ /pubmed/32226089 http://dx.doi.org/10.1016/j.cplett.2012.01.061 Text en Copyright © 2012 Elsevier B.V. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Article
Liu, Liwei
Li, Dongbo
Bai, Fenglan
A relative Lempel–Ziv complexity: Application to comparing biological sequences
title A relative Lempel–Ziv complexity: Application to comparing biological sequences
title_full A relative Lempel–Ziv complexity: Application to comparing biological sequences
title_fullStr A relative Lempel–Ziv complexity: Application to comparing biological sequences
title_full_unstemmed A relative Lempel–Ziv complexity: Application to comparing biological sequences
title_short A relative Lempel–Ziv complexity: Application to comparing biological sequences
title_sort relative lempel–ziv complexity: application to comparing biological sequences
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7094452/
https://www.ncbi.nlm.nih.gov/pubmed/32226089
http://dx.doi.org/10.1016/j.cplett.2012.01.061
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