Applying frequency chaos game representation with perceptual image hashing to gene sequence phylogenetic analyses
As a very important research direction in the field of bioinformatics, sequence alignment plays a vital role in the research and development of biology. Converting genome sequence to graph by using frequency chaos game representation (FCGR) is an excellent gene sequence mapping technology, which can...
Ausführliche Beschreibung
Autor*in: |
Ni, Haiming [verfasserIn] |
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Format: |
E-Artikel |
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Sprache: |
Englisch |
Erschienen: |
2021transfer abstract |
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Schlagwörter: |
Frequency chaos game representation |
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Übergeordnetes Werk: |
Enthalten in: Su1569 Standardized Training Program on Diagnosis of Early Gastrointestinal Cancers Using Narrow Band Imaging (NBI) in Asia - Chiu, Philip W. ELSEVIER, 2015, New York, NY [u.a.] |
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Übergeordnetes Werk: |
volume:107 ; year:2021 ; pages:0 |
Links: |
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DOI / URN: |
10.1016/j.jmgm.2021.107942 |
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Katalog-ID: |
ELV054690897 |
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520 | |a As a very important research direction in the field of bioinformatics, sequence alignment plays a vital role in the research and development of biology. Converting genome sequence to graph by using frequency chaos game representation (FCGR) is an excellent gene sequence mapping technology, which can store rich genetic information into FCGR graphics. To each FCGR image, we construct its perceptual image hashing (PIH) matrix using the bicubic interpolation zooming. The difference of the perceptual hash matrix of each two images is calculated, and the clustering distance of the corresponding two gene sequences is represented by the differentials of the perceptual hash matrix. In this paper, we aligned and analyzed several typical genome sequence datasets including mammalian mitochondrial genes, human immunodeficiency virus 1 (HIV-1) and hepatitis E virus (HEV) to build their evolutionary trees. Experimental results showed that our PIH combining FCGR method (FCGR-PIH) has similar classification accuracy to the classical Clustal W sequence alignment method. Furthermore, 25 complete mitochondrial DNA sequences of cichlid fishes and 27 Escherichia coli/Shigella full genome sequences were selected from the AFproject test platform for tests. The performance benchmark rankings demonstrate the effectiveness of the FCGR-PIH algorithm and its potential for large-scale genome sequence analysis. | ||
520 | |a As a very important research direction in the field of bioinformatics, sequence alignment plays a vital role in the research and development of biology. Converting genome sequence to graph by using frequency chaos game representation (FCGR) is an excellent gene sequence mapping technology, which can store rich genetic information into FCGR graphics. To each FCGR image, we construct its perceptual image hashing (PIH) matrix using the bicubic interpolation zooming. The difference of the perceptual hash matrix of each two images is calculated, and the clustering distance of the corresponding two gene sequences is represented by the differentials of the perceptual hash matrix. In this paper, we aligned and analyzed several typical genome sequence datasets including mammalian mitochondrial genes, human immunodeficiency virus 1 (HIV-1) and hepatitis E virus (HEV) to build their evolutionary trees. Experimental results showed that our PIH combining FCGR method (FCGR-PIH) has similar classification accuracy to the classical Clustal W sequence alignment method. Furthermore, 25 complete mitochondrial DNA sequences of cichlid fishes and 27 Escherichia coli/Shigella full genome sequences were selected from the AFproject test platform for tests. The performance benchmark rankings demonstrate the effectiveness of the FCGR-PIH algorithm and its potential for large-scale genome sequence analysis. | ||
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650 | 7 | |a Frequency chaos game representation |2 Elsevier | |
650 | 7 | |a Phylogenetic tree construction |2 Elsevier | |
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10.1016/j.jmgm.2021.107942 doi /cbs_pica/cbs_olc/import_discovery/elsevier/einzuspielen/GBV00000000001460.pica (DE-627)ELV054690897 (ELSEVIER)S1093-3263(21)00113-3 DE-627 ger DE-627 rakwb eng 610 VZ 600 670 VZ 51.00 bkl Ni, Haiming verfasserin aut Applying frequency chaos game representation with perceptual image hashing to gene sequence phylogenetic analyses 2021transfer abstract nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier As a very important research direction in the field of bioinformatics, sequence alignment plays a vital role in the research and development of biology. Converting genome sequence to graph by using frequency chaos game representation (FCGR) is an excellent gene sequence mapping technology, which can store rich genetic information into FCGR graphics. To each FCGR image, we construct its perceptual image hashing (PIH) matrix using the bicubic interpolation zooming. The difference of the perceptual hash matrix of each two images is calculated, and the clustering distance of the corresponding two gene sequences is represented by the differentials of the perceptual hash matrix. In this paper, we aligned and analyzed several typical genome sequence datasets including mammalian mitochondrial genes, human immunodeficiency virus 1 (HIV-1) and hepatitis E virus (HEV) to build their evolutionary trees. Experimental results showed that our PIH combining FCGR method (FCGR-PIH) has similar classification accuracy to the classical Clustal W sequence alignment method. Furthermore, 25 complete mitochondrial DNA sequences of cichlid fishes and 27 Escherichia coli/Shigella full genome sequences were selected from the AFproject test platform for tests. The performance benchmark rankings demonstrate the effectiveness of the FCGR-PIH algorithm and its potential for large-scale genome sequence analysis. As a very important research direction in the field of bioinformatics, sequence alignment plays a vital role in the research and development of biology. Converting genome sequence to graph by using frequency chaos game representation (FCGR) is an excellent gene sequence mapping technology, which can store rich genetic information into FCGR graphics. To each FCGR image, we construct its perceptual image hashing (PIH) matrix using the bicubic interpolation zooming. The difference of the perceptual hash matrix of each two images is calculated, and the clustering distance of the corresponding two gene sequences is represented by the differentials of the perceptual hash matrix. In this paper, we aligned and analyzed several typical genome sequence datasets including mammalian mitochondrial genes, human immunodeficiency virus 1 (HIV-1) and hepatitis E virus (HEV) to build their evolutionary trees. Experimental results showed that our PIH combining FCGR method (FCGR-PIH) has similar classification accuracy to the classical Clustal W sequence alignment method. Furthermore, 25 complete mitochondrial DNA sequences of cichlid fishes and 27 Escherichia coli/Shigella full genome sequences were selected from the AFproject test platform for tests. The performance benchmark rankings demonstrate the effectiveness of the FCGR-PIH algorithm and its potential for large-scale genome sequence analysis. Genome sequences alignment Elsevier Frequency chaos game representation Elsevier Phylogenetic tree construction Elsevier Perceptual image hashing Elsevier Mu, Hongbo oth Qi, Dawei oth Enthalten in Elsevier Chiu, Philip W. ELSEVIER Su1569 Standardized Training Program on Diagnosis of Early Gastrointestinal Cancers Using Narrow Band Imaging (NBI) in Asia 2015 New York, NY [u.a.] (DE-627)ELV013464361 volume:107 year:2021 pages:0 https://doi.org/10.1016/j.jmgm.2021.107942 Volltext GBV_USEFLAG_U GBV_ELV SYSFLAG_U GBV_ILN_11 GBV_ILN_20 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_65 GBV_ILN_70 GBV_ILN_72 GBV_ILN_206 GBV_ILN_257 GBV_ILN_791 GBV_ILN_2001 GBV_ILN_2002 GBV_ILN_2007 GBV_ILN_2011 GBV_ILN_2012 GBV_ILN_2039 GBV_ILN_2069 GBV_ILN_2127 GBV_ILN_2227 51.00 Werkstoffkunde: Allgemeines VZ AR 107 2021 0 |
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10.1016/j.jmgm.2021.107942 doi /cbs_pica/cbs_olc/import_discovery/elsevier/einzuspielen/GBV00000000001460.pica (DE-627)ELV054690897 (ELSEVIER)S1093-3263(21)00113-3 DE-627 ger DE-627 rakwb eng 610 VZ 600 670 VZ 51.00 bkl Ni, Haiming verfasserin aut Applying frequency chaos game representation with perceptual image hashing to gene sequence phylogenetic analyses 2021transfer abstract nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier As a very important research direction in the field of bioinformatics, sequence alignment plays a vital role in the research and development of biology. Converting genome sequence to graph by using frequency chaos game representation (FCGR) is an excellent gene sequence mapping technology, which can store rich genetic information into FCGR graphics. To each FCGR image, we construct its perceptual image hashing (PIH) matrix using the bicubic interpolation zooming. The difference of the perceptual hash matrix of each two images is calculated, and the clustering distance of the corresponding two gene sequences is represented by the differentials of the perceptual hash matrix. In this paper, we aligned and analyzed several typical genome sequence datasets including mammalian mitochondrial genes, human immunodeficiency virus 1 (HIV-1) and hepatitis E virus (HEV) to build their evolutionary trees. Experimental results showed that our PIH combining FCGR method (FCGR-PIH) has similar classification accuracy to the classical Clustal W sequence alignment method. Furthermore, 25 complete mitochondrial DNA sequences of cichlid fishes and 27 Escherichia coli/Shigella full genome sequences were selected from the AFproject test platform for tests. The performance benchmark rankings demonstrate the effectiveness of the FCGR-PIH algorithm and its potential for large-scale genome sequence analysis. As a very important research direction in the field of bioinformatics, sequence alignment plays a vital role in the research and development of biology. Converting genome sequence to graph by using frequency chaos game representation (FCGR) is an excellent gene sequence mapping technology, which can store rich genetic information into FCGR graphics. To each FCGR image, we construct its perceptual image hashing (PIH) matrix using the bicubic interpolation zooming. The difference of the perceptual hash matrix of each two images is calculated, and the clustering distance of the corresponding two gene sequences is represented by the differentials of the perceptual hash matrix. In this paper, we aligned and analyzed several typical genome sequence datasets including mammalian mitochondrial genes, human immunodeficiency virus 1 (HIV-1) and hepatitis E virus (HEV) to build their evolutionary trees. Experimental results showed that our PIH combining FCGR method (FCGR-PIH) has similar classification accuracy to the classical Clustal W sequence alignment method. Furthermore, 25 complete mitochondrial DNA sequences of cichlid fishes and 27 Escherichia coli/Shigella full genome sequences were selected from the AFproject test platform for tests. The performance benchmark rankings demonstrate the effectiveness of the FCGR-PIH algorithm and its potential for large-scale genome sequence analysis. Genome sequences alignment Elsevier Frequency chaos game representation Elsevier Phylogenetic tree construction Elsevier Perceptual image hashing Elsevier Mu, Hongbo oth Qi, Dawei oth Enthalten in Elsevier Chiu, Philip W. ELSEVIER Su1569 Standardized Training Program on Diagnosis of Early Gastrointestinal Cancers Using Narrow Band Imaging (NBI) in Asia 2015 New York, NY [u.a.] (DE-627)ELV013464361 volume:107 year:2021 pages:0 https://doi.org/10.1016/j.jmgm.2021.107942 Volltext GBV_USEFLAG_U GBV_ELV SYSFLAG_U GBV_ILN_11 GBV_ILN_20 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_65 GBV_ILN_70 GBV_ILN_72 GBV_ILN_206 GBV_ILN_257 GBV_ILN_791 GBV_ILN_2001 GBV_ILN_2002 GBV_ILN_2007 GBV_ILN_2011 GBV_ILN_2012 GBV_ILN_2039 GBV_ILN_2069 GBV_ILN_2127 GBV_ILN_2227 51.00 Werkstoffkunde: Allgemeines VZ AR 107 2021 0 |
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10.1016/j.jmgm.2021.107942 doi /cbs_pica/cbs_olc/import_discovery/elsevier/einzuspielen/GBV00000000001460.pica (DE-627)ELV054690897 (ELSEVIER)S1093-3263(21)00113-3 DE-627 ger DE-627 rakwb eng 610 VZ 600 670 VZ 51.00 bkl Ni, Haiming verfasserin aut Applying frequency chaos game representation with perceptual image hashing to gene sequence phylogenetic analyses 2021transfer abstract nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier As a very important research direction in the field of bioinformatics, sequence alignment plays a vital role in the research and development of biology. Converting genome sequence to graph by using frequency chaos game representation (FCGR) is an excellent gene sequence mapping technology, which can store rich genetic information into FCGR graphics. To each FCGR image, we construct its perceptual image hashing (PIH) matrix using the bicubic interpolation zooming. The difference of the perceptual hash matrix of each two images is calculated, and the clustering distance of the corresponding two gene sequences is represented by the differentials of the perceptual hash matrix. In this paper, we aligned and analyzed several typical genome sequence datasets including mammalian mitochondrial genes, human immunodeficiency virus 1 (HIV-1) and hepatitis E virus (HEV) to build their evolutionary trees. Experimental results showed that our PIH combining FCGR method (FCGR-PIH) has similar classification accuracy to the classical Clustal W sequence alignment method. Furthermore, 25 complete mitochondrial DNA sequences of cichlid fishes and 27 Escherichia coli/Shigella full genome sequences were selected from the AFproject test platform for tests. The performance benchmark rankings demonstrate the effectiveness of the FCGR-PIH algorithm and its potential for large-scale genome sequence analysis. As a very important research direction in the field of bioinformatics, sequence alignment plays a vital role in the research and development of biology. Converting genome sequence to graph by using frequency chaos game representation (FCGR) is an excellent gene sequence mapping technology, which can store rich genetic information into FCGR graphics. To each FCGR image, we construct its perceptual image hashing (PIH) matrix using the bicubic interpolation zooming. The difference of the perceptual hash matrix of each two images is calculated, and the clustering distance of the corresponding two gene sequences is represented by the differentials of the perceptual hash matrix. In this paper, we aligned and analyzed several typical genome sequence datasets including mammalian mitochondrial genes, human immunodeficiency virus 1 (HIV-1) and hepatitis E virus (HEV) to build their evolutionary trees. Experimental results showed that our PIH combining FCGR method (FCGR-PIH) has similar classification accuracy to the classical Clustal W sequence alignment method. Furthermore, 25 complete mitochondrial DNA sequences of cichlid fishes and 27 Escherichia coli/Shigella full genome sequences were selected from the AFproject test platform for tests. The performance benchmark rankings demonstrate the effectiveness of the FCGR-PIH algorithm and its potential for large-scale genome sequence analysis. Genome sequences alignment Elsevier Frequency chaos game representation Elsevier Phylogenetic tree construction Elsevier Perceptual image hashing Elsevier Mu, Hongbo oth Qi, Dawei oth Enthalten in Elsevier Chiu, Philip W. ELSEVIER Su1569 Standardized Training Program on Diagnosis of Early Gastrointestinal Cancers Using Narrow Band Imaging (NBI) in Asia 2015 New York, NY [u.a.] (DE-627)ELV013464361 volume:107 year:2021 pages:0 https://doi.org/10.1016/j.jmgm.2021.107942 Volltext GBV_USEFLAG_U GBV_ELV SYSFLAG_U GBV_ILN_11 GBV_ILN_20 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_65 GBV_ILN_70 GBV_ILN_72 GBV_ILN_206 GBV_ILN_257 GBV_ILN_791 GBV_ILN_2001 GBV_ILN_2002 GBV_ILN_2007 GBV_ILN_2011 GBV_ILN_2012 GBV_ILN_2039 GBV_ILN_2069 GBV_ILN_2127 GBV_ILN_2227 51.00 Werkstoffkunde: Allgemeines VZ AR 107 2021 0 |
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10.1016/j.jmgm.2021.107942 doi /cbs_pica/cbs_olc/import_discovery/elsevier/einzuspielen/GBV00000000001460.pica (DE-627)ELV054690897 (ELSEVIER)S1093-3263(21)00113-3 DE-627 ger DE-627 rakwb eng 610 VZ 600 670 VZ 51.00 bkl Ni, Haiming verfasserin aut Applying frequency chaos game representation with perceptual image hashing to gene sequence phylogenetic analyses 2021transfer abstract nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier As a very important research direction in the field of bioinformatics, sequence alignment plays a vital role in the research and development of biology. Converting genome sequence to graph by using frequency chaos game representation (FCGR) is an excellent gene sequence mapping technology, which can store rich genetic information into FCGR graphics. To each FCGR image, we construct its perceptual image hashing (PIH) matrix using the bicubic interpolation zooming. The difference of the perceptual hash matrix of each two images is calculated, and the clustering distance of the corresponding two gene sequences is represented by the differentials of the perceptual hash matrix. In this paper, we aligned and analyzed several typical genome sequence datasets including mammalian mitochondrial genes, human immunodeficiency virus 1 (HIV-1) and hepatitis E virus (HEV) to build their evolutionary trees. Experimental results showed that our PIH combining FCGR method (FCGR-PIH) has similar classification accuracy to the classical Clustal W sequence alignment method. Furthermore, 25 complete mitochondrial DNA sequences of cichlid fishes and 27 Escherichia coli/Shigella full genome sequences were selected from the AFproject test platform for tests. The performance benchmark rankings demonstrate the effectiveness of the FCGR-PIH algorithm and its potential for large-scale genome sequence analysis. As a very important research direction in the field of bioinformatics, sequence alignment plays a vital role in the research and development of biology. Converting genome sequence to graph by using frequency chaos game representation (FCGR) is an excellent gene sequence mapping technology, which can store rich genetic information into FCGR graphics. To each FCGR image, we construct its perceptual image hashing (PIH) matrix using the bicubic interpolation zooming. The difference of the perceptual hash matrix of each two images is calculated, and the clustering distance of the corresponding two gene sequences is represented by the differentials of the perceptual hash matrix. In this paper, we aligned and analyzed several typical genome sequence datasets including mammalian mitochondrial genes, human immunodeficiency virus 1 (HIV-1) and hepatitis E virus (HEV) to build their evolutionary trees. Experimental results showed that our PIH combining FCGR method (FCGR-PIH) has similar classification accuracy to the classical Clustal W sequence alignment method. Furthermore, 25 complete mitochondrial DNA sequences of cichlid fishes and 27 Escherichia coli/Shigella full genome sequences were selected from the AFproject test platform for tests. The performance benchmark rankings demonstrate the effectiveness of the FCGR-PIH algorithm and its potential for large-scale genome sequence analysis. Genome sequences alignment Elsevier Frequency chaos game representation Elsevier Phylogenetic tree construction Elsevier Perceptual image hashing Elsevier Mu, Hongbo oth Qi, Dawei oth Enthalten in Elsevier Chiu, Philip W. ELSEVIER Su1569 Standardized Training Program on Diagnosis of Early Gastrointestinal Cancers Using Narrow Band Imaging (NBI) in Asia 2015 New York, NY [u.a.] (DE-627)ELV013464361 volume:107 year:2021 pages:0 https://doi.org/10.1016/j.jmgm.2021.107942 Volltext GBV_USEFLAG_U GBV_ELV SYSFLAG_U GBV_ILN_11 GBV_ILN_20 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_65 GBV_ILN_70 GBV_ILN_72 GBV_ILN_206 GBV_ILN_257 GBV_ILN_791 GBV_ILN_2001 GBV_ILN_2002 GBV_ILN_2007 GBV_ILN_2011 GBV_ILN_2012 GBV_ILN_2039 GBV_ILN_2069 GBV_ILN_2127 GBV_ILN_2227 51.00 Werkstoffkunde: Allgemeines VZ AR 107 2021 0 |
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10.1016/j.jmgm.2021.107942 doi /cbs_pica/cbs_olc/import_discovery/elsevier/einzuspielen/GBV00000000001460.pica (DE-627)ELV054690897 (ELSEVIER)S1093-3263(21)00113-3 DE-627 ger DE-627 rakwb eng 610 VZ 600 670 VZ 51.00 bkl Ni, Haiming verfasserin aut Applying frequency chaos game representation with perceptual image hashing to gene sequence phylogenetic analyses 2021transfer abstract nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier As a very important research direction in the field of bioinformatics, sequence alignment plays a vital role in the research and development of biology. Converting genome sequence to graph by using frequency chaos game representation (FCGR) is an excellent gene sequence mapping technology, which can store rich genetic information into FCGR graphics. To each FCGR image, we construct its perceptual image hashing (PIH) matrix using the bicubic interpolation zooming. The difference of the perceptual hash matrix of each two images is calculated, and the clustering distance of the corresponding two gene sequences is represented by the differentials of the perceptual hash matrix. In this paper, we aligned and analyzed several typical genome sequence datasets including mammalian mitochondrial genes, human immunodeficiency virus 1 (HIV-1) and hepatitis E virus (HEV) to build their evolutionary trees. Experimental results showed that our PIH combining FCGR method (FCGR-PIH) has similar classification accuracy to the classical Clustal W sequence alignment method. Furthermore, 25 complete mitochondrial DNA sequences of cichlid fishes and 27 Escherichia coli/Shigella full genome sequences were selected from the AFproject test platform for tests. The performance benchmark rankings demonstrate the effectiveness of the FCGR-PIH algorithm and its potential for large-scale genome sequence analysis. As a very important research direction in the field of bioinformatics, sequence alignment plays a vital role in the research and development of biology. Converting genome sequence to graph by using frequency chaos game representation (FCGR) is an excellent gene sequence mapping technology, which can store rich genetic information into FCGR graphics. To each FCGR image, we construct its perceptual image hashing (PIH) matrix using the bicubic interpolation zooming. The difference of the perceptual hash matrix of each two images is calculated, and the clustering distance of the corresponding two gene sequences is represented by the differentials of the perceptual hash matrix. In this paper, we aligned and analyzed several typical genome sequence datasets including mammalian mitochondrial genes, human immunodeficiency virus 1 (HIV-1) and hepatitis E virus (HEV) to build their evolutionary trees. Experimental results showed that our PIH combining FCGR method (FCGR-PIH) has similar classification accuracy to the classical Clustal W sequence alignment method. Furthermore, 25 complete mitochondrial DNA sequences of cichlid fishes and 27 Escherichia coli/Shigella full genome sequences were selected from the AFproject test platform for tests. The performance benchmark rankings demonstrate the effectiveness of the FCGR-PIH algorithm and its potential for large-scale genome sequence analysis. Genome sequences alignment Elsevier Frequency chaos game representation Elsevier Phylogenetic tree construction Elsevier Perceptual image hashing Elsevier Mu, Hongbo oth Qi, Dawei oth Enthalten in Elsevier Chiu, Philip W. ELSEVIER Su1569 Standardized Training Program on Diagnosis of Early Gastrointestinal Cancers Using Narrow Band Imaging (NBI) in Asia 2015 New York, NY [u.a.] (DE-627)ELV013464361 volume:107 year:2021 pages:0 https://doi.org/10.1016/j.jmgm.2021.107942 Volltext GBV_USEFLAG_U GBV_ELV SYSFLAG_U GBV_ILN_11 GBV_ILN_20 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_65 GBV_ILN_70 GBV_ILN_72 GBV_ILN_206 GBV_ILN_257 GBV_ILN_791 GBV_ILN_2001 GBV_ILN_2002 GBV_ILN_2007 GBV_ILN_2011 GBV_ILN_2012 GBV_ILN_2039 GBV_ILN_2069 GBV_ILN_2127 GBV_ILN_2227 51.00 Werkstoffkunde: Allgemeines VZ AR 107 2021 0 |
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applying frequency chaos game representation with perceptual image hashing to gene sequence phylogenetic analyses |
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Applying frequency chaos game representation with perceptual image hashing to gene sequence phylogenetic analyses |
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As a very important research direction in the field of bioinformatics, sequence alignment plays a vital role in the research and development of biology. Converting genome sequence to graph by using frequency chaos game representation (FCGR) is an excellent gene sequence mapping technology, which can store rich genetic information into FCGR graphics. To each FCGR image, we construct its perceptual image hashing (PIH) matrix using the bicubic interpolation zooming. The difference of the perceptual hash matrix of each two images is calculated, and the clustering distance of the corresponding two gene sequences is represented by the differentials of the perceptual hash matrix. In this paper, we aligned and analyzed several typical genome sequence datasets including mammalian mitochondrial genes, human immunodeficiency virus 1 (HIV-1) and hepatitis E virus (HEV) to build their evolutionary trees. Experimental results showed that our PIH combining FCGR method (FCGR-PIH) has similar classification accuracy to the classical Clustal W sequence alignment method. Furthermore, 25 complete mitochondrial DNA sequences of cichlid fishes and 27 Escherichia coli/Shigella full genome sequences were selected from the AFproject test platform for tests. The performance benchmark rankings demonstrate the effectiveness of the FCGR-PIH algorithm and its potential for large-scale genome sequence analysis. |
abstractGer |
As a very important research direction in the field of bioinformatics, sequence alignment plays a vital role in the research and development of biology. Converting genome sequence to graph by using frequency chaos game representation (FCGR) is an excellent gene sequence mapping technology, which can store rich genetic information into FCGR graphics. To each FCGR image, we construct its perceptual image hashing (PIH) matrix using the bicubic interpolation zooming. The difference of the perceptual hash matrix of each two images is calculated, and the clustering distance of the corresponding two gene sequences is represented by the differentials of the perceptual hash matrix. In this paper, we aligned and analyzed several typical genome sequence datasets including mammalian mitochondrial genes, human immunodeficiency virus 1 (HIV-1) and hepatitis E virus (HEV) to build their evolutionary trees. Experimental results showed that our PIH combining FCGR method (FCGR-PIH) has similar classification accuracy to the classical Clustal W sequence alignment method. Furthermore, 25 complete mitochondrial DNA sequences of cichlid fishes and 27 Escherichia coli/Shigella full genome sequences were selected from the AFproject test platform for tests. The performance benchmark rankings demonstrate the effectiveness of the FCGR-PIH algorithm and its potential for large-scale genome sequence analysis. |
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As a very important research direction in the field of bioinformatics, sequence alignment plays a vital role in the research and development of biology. Converting genome sequence to graph by using frequency chaos game representation (FCGR) is an excellent gene sequence mapping technology, which can store rich genetic information into FCGR graphics. To each FCGR image, we construct its perceptual image hashing (PIH) matrix using the bicubic interpolation zooming. The difference of the perceptual hash matrix of each two images is calculated, and the clustering distance of the corresponding two gene sequences is represented by the differentials of the perceptual hash matrix. In this paper, we aligned and analyzed several typical genome sequence datasets including mammalian mitochondrial genes, human immunodeficiency virus 1 (HIV-1) and hepatitis E virus (HEV) to build their evolutionary trees. Experimental results showed that our PIH combining FCGR method (FCGR-PIH) has similar classification accuracy to the classical Clustal W sequence alignment method. Furthermore, 25 complete mitochondrial DNA sequences of cichlid fishes and 27 Escherichia coli/Shigella full genome sequences were selected from the AFproject test platform for tests. The performance benchmark rankings demonstrate the effectiveness of the FCGR-PIH algorithm and its potential for large-scale genome sequence analysis. |
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Applying frequency chaos game representation with perceptual image hashing to gene sequence phylogenetic analyses |
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The difference of the perceptual hash matrix of each two images is calculated, and the clustering distance of the corresponding two gene sequences is represented by the differentials of the perceptual hash matrix. In this paper, we aligned and analyzed several typical genome sequence datasets including mammalian mitochondrial genes, human immunodeficiency virus 1 (HIV-1) and hepatitis E virus (HEV) to build their evolutionary trees. Experimental results showed that our PIH combining FCGR method (FCGR-PIH) has similar classification accuracy to the classical Clustal W sequence alignment method. Furthermore, 25 complete mitochondrial DNA sequences of cichlid fishes and 27 Escherichia coli/Shigella full genome sequences were selected from the AFproject test platform for tests. 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