New method for global alignment of 2 DNA sequences by the tree data structure

We introduce a new approach to investigate problem of DNA sequence alignment. The method consists of three parts: (i) simple alignment algorithm, (ii) extension algorithm for largest common substring, (iii) graphical simple alignment tree (GSA tree). The approach firstly obtains a graphical represen...

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Detalles Bibliográficos
Autores principales: Qi, Zhao-Hui, Qi, Xiao-Qin, Liu, Chen-Chen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Published by Elsevier Ltd. 2010
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7094160/
https://www.ncbi.nlm.nih.gov/pubmed/20025888
http://dx.doi.org/10.1016/j.jtbi.2009.12.012
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author Qi, Zhao-Hui
Qi, Xiao-Qin
Liu, Chen-Chen
author_facet Qi, Zhao-Hui
Qi, Xiao-Qin
Liu, Chen-Chen
author_sort Qi, Zhao-Hui
collection PubMed
description We introduce a new approach to investigate problem of DNA sequence alignment. The method consists of three parts: (i) simple alignment algorithm, (ii) extension algorithm for largest common substring, (iii) graphical simple alignment tree (GSA tree). The approach firstly obtains a graphical representation of scores of DNA sequences by the scoring equation [Formula: see text]. Then a GSA tree is constructed to facilitate solving the problem for global alignment of 2 DNA sequences. Finally we give several practical examples to illustrate the utility and practicality of the approach.
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spelling pubmed-70941602020-03-25 New method for global alignment of 2 DNA sequences by the tree data structure Qi, Zhao-Hui Qi, Xiao-Qin Liu, Chen-Chen J Theor Biol Article We introduce a new approach to investigate problem of DNA sequence alignment. The method consists of three parts: (i) simple alignment algorithm, (ii) extension algorithm for largest common substring, (iii) graphical simple alignment tree (GSA tree). The approach firstly obtains a graphical representation of scores of DNA sequences by the scoring equation [Formula: see text]. Then a GSA tree is constructed to facilitate solving the problem for global alignment of 2 DNA sequences. Finally we give several practical examples to illustrate the utility and practicality of the approach. Published by Elsevier Ltd. 2010-03-21 2009-12-16 /pmc/articles/PMC7094160/ /pubmed/20025888 http://dx.doi.org/10.1016/j.jtbi.2009.12.012 Text en Crown copyright © 2009 Published by Elsevier Ltd. 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
Qi, Zhao-Hui
Qi, Xiao-Qin
Liu, Chen-Chen
New method for global alignment of 2 DNA sequences by the tree data structure
title New method for global alignment of 2 DNA sequences by the tree data structure
title_full New method for global alignment of 2 DNA sequences by the tree data structure
title_fullStr New method for global alignment of 2 DNA sequences by the tree data structure
title_full_unstemmed New method for global alignment of 2 DNA sequences by the tree data structure
title_short New method for global alignment of 2 DNA sequences by the tree data structure
title_sort new method for global alignment of 2 dna sequences by the tree data structure
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7094160/
https://www.ncbi.nlm.nih.gov/pubmed/20025888
http://dx.doi.org/10.1016/j.jtbi.2009.12.012
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