TY - GEN
T1 - AlignScope
T2 - 4th Asia-Pacific Bioinformatics Conference, APBC 2006
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
Y2 - 13 February 2006 through 16 February 2006
ER -