A Gene Clustering Method with Hierarchical Visualization of Alignment Pairs

KIPS Transactions on Software and Data Engineering, Vol. 16, No. 3, pp. 143-152, Mar. 2009
10.3745/KIPSTA.2009.16.3.143, Full Text:


One of the main issues in comparative genomics is to study chromosomal gene order in one or more related species. For this purpose, the whole genome alignment is usually applied to find the horizontal gene transfer, gene duplication, and gene loss between two related genomes. Also it is well known that the novel visualization tool with whole genome alignment is greatly useful for us to understand genome organization and evolution process. There are a lot of algorithms and visualization tools already proposed to find the “gene clusters” on genome alignments. But due to the huge size of whole genome, the previous visualization tools are not convenient to discover the relationship between two genomes. In this paper, we propose AlignScope, a novel visualization system for whole genome alignment, especially useful to find gene clusters between two aligned genomes. This AlignScope not only provides the simplified structure of genome alignment at any simplified level, but also helps us to find gene clusters. In experiment, we show the performance of AlignScope with several microbial genomes such as B. subtilis, B.halodurans, E. coli K12, and M. tuberculosis H37Rv, which have more than 5000 alignment pairs (matched DNA subsequence).

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Cite this article
[IEEE Style]
H. J. Jin, S. H. Park and H. G. Cho, "A Gene Clustering Method with Hierarchical Visualization of Alignment Pairs," KIPS Journal A (2001 ~ 2012) , vol. 16, no. 3, pp. 143-152, 2009. DOI: 10.3745/KIPSTA.2009.16.3.143.

[ACM Style]
Hee Jeong Jin, Su Hyun Park, and Hwan Gue Cho. 2009. A Gene Clustering Method with Hierarchical Visualization of Alignment Pairs. KIPS Journal A (2001 ~ 2012) , 16, 3, (2009), 143-152. DOI: 10.3745/KIPSTA.2009.16.3.143.