AlignScope: A visual mining tool for gene team finding with whole genome alignment

Hee Jeong Jin, Hye Jung Kim, Jeong-Hyeon Choi, Hwan Gue Cho

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

One of the main issues in comparative genomics is the study of chromosomal gene order in one or more related species. Recently identifying sets of orthologous genes in several genomes has become getting important, since a cluster of similar genes helps us to predict the function of unknown genes. For this purpose, the whole genome alignment is usually used to determine horizontal gene transfer, gene duplication, and gene loss between two related genomes. Also it is well known that a novel visualization tool of the whole genome alignment would be very useful for understanding genome organization and the evolutionary process. In this paper, we propose a method for identifying and visualizing the alignment of the whole genome alignment, especially for detecting gene clusters between two aligned genomes. Since the current rigorous algorithm for finding gene clusters has strong and artificial constraints, they are not useful for coping with "noisy" alignments. We developed the system AlignScope to provide a simplified structure for genome alignment at any level, and also to help us to find gene clusters. In this experiment, we have tested AlignScope on several microbial genomes.

Original languageEnglish (US)
Title of host publicationProceedings of the 4th Asia-Pacific Bioinformatics Conference, APBC 2006
Pages69-78
Number of pages10
StatePublished - Dec 1 2006
Event4th Asia-Pacific Bioinformatics Conference, APBC 2006 - Taipei, Taiwan, Province of China
Duration: Feb 13 2006Feb 16 2006

Publication series

NameSeries on Advances in Bioinformatics and Computational Biology
Volume3
ISSN (Print)1751-6404

Other

Other4th Asia-Pacific Bioinformatics Conference, APBC 2006
CountryTaiwan, Province of China
CityTaipei
Period2/13/062/16/06

Fingerprint

Genes
Gene transfer
Visualization

ASJC Scopus subject areas

  • Bioengineering
  • Information Systems

Cite this

Jin, H. J., Kim, H. J., Choi, J-H., & Cho, H. G. (2006). AlignScope: A visual mining tool for gene team finding with whole genome alignment. In Proceedings of the 4th Asia-Pacific Bioinformatics Conference, APBC 2006 (pp. 69-78). (Series on Advances in Bioinformatics and Computational Biology; Vol. 3).

AlignScope : A visual mining tool for gene team finding with whole genome alignment. / Jin, Hee Jeong; Kim, Hye Jung; Choi, Jeong-Hyeon; Cho, Hwan Gue.

Proceedings of the 4th Asia-Pacific Bioinformatics Conference, APBC 2006. 2006. p. 69-78 (Series on Advances in Bioinformatics and Computational Biology; Vol. 3).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Jin, HJ, Kim, HJ, Choi, J-H & Cho, HG 2006, AlignScope: A visual mining tool for gene team finding with whole genome alignment. in Proceedings of the 4th Asia-Pacific Bioinformatics Conference, APBC 2006. Series on Advances in Bioinformatics and Computational Biology, vol. 3, pp. 69-78, 4th Asia-Pacific Bioinformatics Conference, APBC 2006, Taipei, Taiwan, Province of China, 2/13/06.
Jin HJ, Kim HJ, Choi J-H, Cho HG. AlignScope: A visual mining tool for gene team finding with whole genome alignment. In Proceedings of the 4th Asia-Pacific Bioinformatics Conference, APBC 2006. 2006. p. 69-78. (Series on Advances in Bioinformatics and Computational Biology).
Jin, Hee Jeong ; Kim, Hye Jung ; Choi, Jeong-Hyeon ; Cho, Hwan Gue. / AlignScope : A visual mining tool for gene team finding with whole genome alignment. Proceedings of the 4th Asia-Pacific Bioinformatics Conference, APBC 2006. 2006. pp. 69-78 (Series on Advances in Bioinformatics and Computational Biology).
@inproceedings{1dd36d0ccfc44ab490c0f179facfa095,
title = "AlignScope: A visual mining tool for gene team finding with whole genome alignment",
abstract = "One of the main issues in comparative genomics is the study of chromosomal gene order in one or more related species. Recently identifying sets of orthologous genes in several genomes has become getting important, since a cluster of similar genes helps us to predict the function of unknown genes. For this purpose, the whole genome alignment is usually used to determine horizontal gene transfer, gene duplication, and gene loss between two related genomes. Also it is well known that a novel visualization tool of the whole genome alignment would be very useful for understanding genome organization and the evolutionary process. In this paper, we propose a method for identifying and visualizing the alignment of the whole genome alignment, especially for detecting gene clusters between two aligned genomes. Since the current rigorous algorithm for finding gene clusters has strong and artificial constraints, they are not useful for coping with {"}noisy{"} alignments. We developed the system AlignScope to provide a simplified structure for genome alignment at any level, and also to help us to find gene clusters. In this experiment, we have tested AlignScope on several microbial genomes.",
author = "Jin, {Hee Jeong} and Kim, {Hye Jung} and Jeong-Hyeon Choi and Cho, {Hwan Gue}",
year = "2006",
month = "12",
day = "1",
language = "English (US)",
isbn = "1860946232",
series = "Series on Advances in Bioinformatics and Computational Biology",
pages = "69--78",
booktitle = "Proceedings of the 4th Asia-Pacific Bioinformatics Conference, APBC 2006",

}

TY - GEN

T1 - AlignScope

T2 - A visual mining tool for gene team finding with whole genome alignment

AU - Jin, Hee Jeong

AU - Kim, Hye Jung

AU - Choi, Jeong-Hyeon

AU - Cho, Hwan Gue

PY - 2006/12/1

Y1 - 2006/12/1

N2 - One of the main issues in comparative genomics is the study of chromosomal gene order in one or more related species. Recently identifying sets of orthologous genes in several genomes has become getting important, since a cluster of similar genes helps us to predict the function of unknown genes. For this purpose, the whole genome alignment is usually used to determine horizontal gene transfer, gene duplication, and gene loss between two related genomes. Also it is well known that a novel visualization tool of the whole genome alignment would be very useful for understanding genome organization and the evolutionary process. In this paper, we propose a method for identifying and visualizing the alignment of the whole genome alignment, especially for detecting gene clusters between two aligned genomes. Since the current rigorous algorithm for finding gene clusters has strong and artificial constraints, they are not useful for coping with "noisy" alignments. We developed the system AlignScope to provide a simplified structure for genome alignment at any level, and also to help us to find gene clusters. In this experiment, we have tested AlignScope on several microbial genomes.

AB - One of the main issues in comparative genomics is the study of chromosomal gene order in one or more related species. Recently identifying sets of orthologous genes in several genomes has become getting important, since a cluster of similar genes helps us to predict the function of unknown genes. For this purpose, the whole genome alignment is usually used to determine horizontal gene transfer, gene duplication, and gene loss between two related genomes. Also it is well known that a novel visualization tool of the whole genome alignment would be very useful for understanding genome organization and the evolutionary process. In this paper, we propose a method for identifying and visualizing the alignment of the whole genome alignment, especially for detecting gene clusters between two aligned genomes. Since the current rigorous algorithm for finding gene clusters has strong and artificial constraints, they are not useful for coping with "noisy" alignments. We developed the system AlignScope to provide a simplified structure for genome alignment at any level, and also to help us to find gene clusters. In this experiment, we have tested AlignScope on several microbial genomes.

UR - http://www.scopus.com/inward/record.url?scp=84863050007&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84863050007&partnerID=8YFLogxK

M3 - Conference contribution

AN - SCOPUS:84863050007

SN - 1860946232

SN - 9781860946233

T3 - Series on Advances in Bioinformatics and Computational Biology

SP - 69

EP - 78

BT - Proceedings of the 4th Asia-Pacific Bioinformatics Conference, APBC 2006

ER -