GenomeFingerprinter: the genome fingerprint and the universal genome fingerprint analysis for systematic comparative genomics.

<h4>Background</h4>No attention has been paid on comparing a set of genome sequences crossing genetic components and biological categories with far divergence over large size range. We define it as the systematic comparative genomics and aim to develop the methodology.<h4>Results&l...

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Autores principales:	Yuncan Ai, Hannan Ai, Fanmei Meng, Lei Zhao
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/631e982895604f5186b21e3acfbe9397
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spelling	oai:doaj.org-article:631e982895604f5186b21e3acfbe93972021-11-18T08:49:08ZGenomeFingerprinter: the genome fingerprint and the universal genome fingerprint analysis for systematic comparative genomics.1932-620310.1371/journal.pone.0077912https://doaj.org/article/631e982895604f5186b21e3acfbe93972013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24205026/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>No attention has been paid on comparing a set of genome sequences crossing genetic components and biological categories with far divergence over large size range. We define it as the systematic comparative genomics and aim to develop the methodology.<h4>Results</h4>First, we create a method, GenomeFingerprinter, to unambiguously produce a set of three-dimensional coordinates from a sequence, followed by one three-dimensional plot and six two-dimensional trajectory projections, to illustrate the genome fingerprint of a given genome sequence. Second, we develop a set of concepts and tools, and thereby establish a method called the universal genome fingerprint analysis (UGFA). Particularly, we define the total genetic component configuration (TGCC) (including chromosome, plasmid, and phage) for describing a strain as a systematic unit, the universal genome fingerprint map (UGFM) of TGCC for differentiating strains as a universal system, and the systematic comparative genomics (SCG) for comparing a set of genomes crossing genetic components and biological categories. Third, we construct a method of quantitative analysis to compare two genomes by using the outcome dataset of genome fingerprint analysis. Specifically, we define the geometric center and its geometric mean for a given genome fingerprint map, followed by the Euclidean distance, the differentiate rate, and the weighted differentiate rate to quantitatively describe the difference between two genomes of comparison. Moreover, we demonstrate the applications through case studies on various genome sequences, giving tremendous insights into the critical issues in microbial genomics and taxonomy.<h4>Conclusions</h4>We have created a method, GenomeFingerprinter, for rapidly computing, geometrically visualizing, intuitively comparing a set of genomes at genome fingerprint level, and hence established a method called the universal genome fingerprint analysis, as well as developed a method of quantitative analysis of the outcome dataset. These have set up the methodology of systematic comparative genomics based on the genome fingerprint analysis.Yuncan AiHannan AiFanmei MengLei ZhaoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 10, p e77912 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yuncan Ai Hannan Ai Fanmei Meng Lei Zhao GenomeFingerprinter: the genome fingerprint and the universal genome fingerprint analysis for systematic comparative genomics.
description	<h4>Background</h4>No attention has been paid on comparing a set of genome sequences crossing genetic components and biological categories with far divergence over large size range. We define it as the systematic comparative genomics and aim to develop the methodology.<h4>Results</h4>First, we create a method, GenomeFingerprinter, to unambiguously produce a set of three-dimensional coordinates from a sequence, followed by one three-dimensional plot and six two-dimensional trajectory projections, to illustrate the genome fingerprint of a given genome sequence. Second, we develop a set of concepts and tools, and thereby establish a method called the universal genome fingerprint analysis (UGFA). Particularly, we define the total genetic component configuration (TGCC) (including chromosome, plasmid, and phage) for describing a strain as a systematic unit, the universal genome fingerprint map (UGFM) of TGCC for differentiating strains as a universal system, and the systematic comparative genomics (SCG) for comparing a set of genomes crossing genetic components and biological categories. Third, we construct a method of quantitative analysis to compare two genomes by using the outcome dataset of genome fingerprint analysis. Specifically, we define the geometric center and its geometric mean for a given genome fingerprint map, followed by the Euclidean distance, the differentiate rate, and the weighted differentiate rate to quantitatively describe the difference between two genomes of comparison. Moreover, we demonstrate the applications through case studies on various genome sequences, giving tremendous insights into the critical issues in microbial genomics and taxonomy.<h4>Conclusions</h4>We have created a method, GenomeFingerprinter, for rapidly computing, geometrically visualizing, intuitively comparing a set of genomes at genome fingerprint level, and hence established a method called the universal genome fingerprint analysis, as well as developed a method of quantitative analysis of the outcome dataset. These have set up the methodology of systematic comparative genomics based on the genome fingerprint analysis.
format	article
author	Yuncan Ai Hannan Ai Fanmei Meng Lei Zhao
author_facet	Yuncan Ai Hannan Ai Fanmei Meng Lei Zhao
author_sort	Yuncan Ai
title	GenomeFingerprinter: the genome fingerprint and the universal genome fingerprint analysis for systematic comparative genomics.
title_short	GenomeFingerprinter: the genome fingerprint and the universal genome fingerprint analysis for systematic comparative genomics.
title_full	GenomeFingerprinter: the genome fingerprint and the universal genome fingerprint analysis for systematic comparative genomics.
title_fullStr	GenomeFingerprinter: the genome fingerprint and the universal genome fingerprint analysis for systematic comparative genomics.
title_full_unstemmed	GenomeFingerprinter: the genome fingerprint and the universal genome fingerprint analysis for systematic comparative genomics.
title_sort	genomefingerprinter: the genome fingerprint and the universal genome fingerprint analysis for systematic comparative genomics.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/631e982895604f5186b21e3acfbe9397
work_keys_str_mv	AT yuncanai genomefingerprinterthegenomefingerprintandtheuniversalgenomefingerprintanalysisforsystematiccomparativegenomics AT hannanai genomefingerprinterthegenomefingerprintandtheuniversalgenomefingerprintanalysisforsystematiccomparativegenomics AT fanmeimeng genomefingerprinterthegenomefingerprintandtheuniversalgenomefingerprintanalysisforsystematiccomparativegenomics AT leizhao genomefingerprinterthegenomefingerprintandtheuniversalgenomefingerprintanalysisforsystematiccomparativegenomics
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GenomeFingerprinter: the genome fingerprint and the universal genome fingerprint analysis for systematic comparative genomics.

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