AlignScope: A Visual Mining Tool for Gene Team Finding with Whole Genome Alignment

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. Alignment is a procedure that compares two or more sequences by searching for a series of individual characters or character patterns that are in the same order in the sequences. This procedure assists in designating the functions of unknown proteins, determining the relatedness of organisms, and identifying structurally and functionally important elements and other useful functions. 9;12 Many widely divergent organisms are descended from a common ancestor through a process called evolution. The inheritance patterns and diversities of these organisms have significant information regarding the nature of small and large-scale evolutionary events. The complexity and the size of the genome make it difficult to analyze. Because the large amount of biological noises is present when visualizing genomes, it is not enough to simply draw the aligned pairs of various genomes. Therefore an alignment visualization tool needs to provide a method for viewing the global structure of whole genome alignment in a simplified form at any level of detail. Figure-1 clearly illustrates this problem. In Figure-1, the resolution of the snapshot is 800 by 600 pixels, so one pixel corresponds about 6000 bases of a given genome sequence. Currently there are several systems for visualizing the alignment of genomes. The NCBI Map Viewer 14 provides graphical displays of biological features on NCBI’s as