Analysis of genome by visualization of genomic signature

Jeong-Hyeon Choi, Seok Ki Lee, Su Bog Yee, Yung Jin Kim, Hwan Gue Cho, Kyu Won Kim

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

The concept of Genomic Signature (GS) is recently established to use as a method of analyzing genome of various species. This concept is pattern of unique base concentration, which is constructed whole genome of biological species. In order to visualize the GS, k-mer program which is based on the method of Chaos Game Representation (CGR) was used to analyze whole genome of various species. The data set used in this study was obtained from NCBI GenBank database and the analysis of GS using the data set compared similarity patterns of various signature lengths and was then visualized through k-mer graph. The k-mer graph allows depiction of frequencies of oligonucleotides in the form of image. As results, the k-mer graph of GS pattern was meaningful by being displayed in hexamer graph about various k lengths. Then we analyzed species-unique patterns of prokaryotic and eukaryotic genomes. We found the pattern of GS was maintained in 30 Kb length, which is less than 100 Kb length which is known as the length of GS in previous reports and the species-unique pattern among chromosomes in eukaryotes having several chromosomes. Therefore, we suggest that the analysis of GS by visualization of k-mer program may provide the clue to solve evolutionary relationship between species and component mechanisms of DNA maintenance.

Original languageEnglish (US)
Pages (from-to)97-104
Number of pages8
JournalKorean Journal of Genetics
Volume24
Issue number1
StatePublished - Mar 1 2002

Fingerprint

Visualization
Genes
Genome
Chromosomes
Nucleic Acid Databases
Eukaryota
Oligonucleotides
Chaos theory
Maintenance
Databases
DNA
Datasets

Keywords

  • Chaos Game Representation
  • Genome
  • Genomic signature
  • K-mer

ASJC Scopus subject areas

  • Genetics

Cite this

Choi, J-H., Lee, S. K., Yee, S. B., Kim, Y. J., Cho, H. G., & Kim, K. W. (2002). Analysis of genome by visualization of genomic signature. Korean Journal of Genetics, 24(1), 97-104.

Analysis of genome by visualization of genomic signature. / Choi, Jeong-Hyeon; Lee, Seok Ki; Yee, Su Bog; Kim, Yung Jin; Cho, Hwan Gue; Kim, Kyu Won.

In: Korean Journal of Genetics, Vol. 24, No. 1, 01.03.2002, p. 97-104.

Research output: Contribution to journalArticle

Choi, J-H, Lee, SK, Yee, SB, Kim, YJ, Cho, HG & Kim, KW 2002, 'Analysis of genome by visualization of genomic signature', Korean Journal of Genetics, vol. 24, no. 1, pp. 97-104.
Choi J-H, Lee SK, Yee SB, Kim YJ, Cho HG, Kim KW. Analysis of genome by visualization of genomic signature. Korean Journal of Genetics. 2002 Mar 1;24(1):97-104.
Choi, Jeong-Hyeon ; Lee, Seok Ki ; Yee, Su Bog ; Kim, Yung Jin ; Cho, Hwan Gue ; Kim, Kyu Won. / Analysis of genome by visualization of genomic signature. In: Korean Journal of Genetics. 2002 ; Vol. 24, No. 1. pp. 97-104.
@article{708922db893145a8b20ed16322eebf5d,
title = "Analysis of genome by visualization of genomic signature",
abstract = "The concept of Genomic Signature (GS) is recently established to use as a method of analyzing genome of various species. This concept is pattern of unique base concentration, which is constructed whole genome of biological species. In order to visualize the GS, k-mer program which is based on the method of Chaos Game Representation (CGR) was used to analyze whole genome of various species. The data set used in this study was obtained from NCBI GenBank database and the analysis of GS using the data set compared similarity patterns of various signature lengths and was then visualized through k-mer graph. The k-mer graph allows depiction of frequencies of oligonucleotides in the form of image. As results, the k-mer graph of GS pattern was meaningful by being displayed in hexamer graph about various k lengths. Then we analyzed species-unique patterns of prokaryotic and eukaryotic genomes. We found the pattern of GS was maintained in 30 Kb length, which is less than 100 Kb length which is known as the length of GS in previous reports and the species-unique pattern among chromosomes in eukaryotes having several chromosomes. Therefore, we suggest that the analysis of GS by visualization of k-mer program may provide the clue to solve evolutionary relationship between species and component mechanisms of DNA maintenance.",
keywords = "Chaos Game Representation, Genome, Genomic signature, K-mer",
author = "Jeong-Hyeon Choi and Lee, {Seok Ki} and Yee, {Su Bog} and Kim, {Yung Jin} and Cho, {Hwan Gue} and Kim, {Kyu Won}",
year = "2002",
month = "3",
day = "1",
language = "English (US)",
volume = "24",
pages = "97--104",
journal = "Genes and Genomics",
issn = "1976-9571",
publisher = "Springer Verlag",
number = "1",

}

TY - JOUR

T1 - Analysis of genome by visualization of genomic signature

AU - Choi, Jeong-Hyeon

AU - Lee, Seok Ki

AU - Yee, Su Bog

AU - Kim, Yung Jin

AU - Cho, Hwan Gue

AU - Kim, Kyu Won

PY - 2002/3/1

Y1 - 2002/3/1

N2 - The concept of Genomic Signature (GS) is recently established to use as a method of analyzing genome of various species. This concept is pattern of unique base concentration, which is constructed whole genome of biological species. In order to visualize the GS, k-mer program which is based on the method of Chaos Game Representation (CGR) was used to analyze whole genome of various species. The data set used in this study was obtained from NCBI GenBank database and the analysis of GS using the data set compared similarity patterns of various signature lengths and was then visualized through k-mer graph. The k-mer graph allows depiction of frequencies of oligonucleotides in the form of image. As results, the k-mer graph of GS pattern was meaningful by being displayed in hexamer graph about various k lengths. Then we analyzed species-unique patterns of prokaryotic and eukaryotic genomes. We found the pattern of GS was maintained in 30 Kb length, which is less than 100 Kb length which is known as the length of GS in previous reports and the species-unique pattern among chromosomes in eukaryotes having several chromosomes. Therefore, we suggest that the analysis of GS by visualization of k-mer program may provide the clue to solve evolutionary relationship between species and component mechanisms of DNA maintenance.

AB - The concept of Genomic Signature (GS) is recently established to use as a method of analyzing genome of various species. This concept is pattern of unique base concentration, which is constructed whole genome of biological species. In order to visualize the GS, k-mer program which is based on the method of Chaos Game Representation (CGR) was used to analyze whole genome of various species. The data set used in this study was obtained from NCBI GenBank database and the analysis of GS using the data set compared similarity patterns of various signature lengths and was then visualized through k-mer graph. The k-mer graph allows depiction of frequencies of oligonucleotides in the form of image. As results, the k-mer graph of GS pattern was meaningful by being displayed in hexamer graph about various k lengths. Then we analyzed species-unique patterns of prokaryotic and eukaryotic genomes. We found the pattern of GS was maintained in 30 Kb length, which is less than 100 Kb length which is known as the length of GS in previous reports and the species-unique pattern among chromosomes in eukaryotes having several chromosomes. Therefore, we suggest that the analysis of GS by visualization of k-mer program may provide the clue to solve evolutionary relationship between species and component mechanisms of DNA maintenance.

KW - Chaos Game Representation

KW - Genome

KW - Genomic signature

KW - K-mer

UR - http://www.scopus.com/inward/record.url?scp=0036111431&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0036111431&partnerID=8YFLogxK

M3 - Article

VL - 24

SP - 97

EP - 104

JO - Genes and Genomics

JF - Genes and Genomics

SN - 1976-9571

IS - 1

ER -