System Overview 

- Input

o Accumulated frequency file all combined piarwise results(*.histogram), which are loaded when open file window.

o COGs and gene files

o DNA sequence files

o Processing : extracting matched regions, combining the relationship between conserved regions and constructing the relation graph.

- Output & Control

o View Tab

§ Show accumulated frequency of matched region and average score

§ Show the number of genomes have overlapped region.

§ Show the COGs and gene, also the name

§ Link other genome : to construct the relation graph.

· It is controlled by the depth selection box on the menu bar over of main screen.

o List  Tab

§ Show the list of edges of relation graph.

§ If you select a edge, you can see the path of the graph to the root on different window(path view window).

§ In the path view window, you can see the DNA sequence of block if you click it. Its sequence can be handle by copy and past.

o STAT Tab

§ Small statistics among the selected genomes.

o FILTER Tab

§ Set the cut_off score for making Block Node.

§ Set the cut_off score to control edge connectivity.

- Filtering the edges given minimum and maximum cut_off scores.

- Filtering the edges given length of block node.

- Selecting the best hit score

o Divided Zooming control(x-axis)

§ The 1^st  bar :  to control  from1/000  to 1/5000 .

§ The 2^nd bar : to control from 1/100 to 1/900.

§ The 3^rd bar  : to control from 1 to 1/10.

o Depth selection button

§ Show the depth of a selected region(reference block) of relation graph.

o Color reverse

§ Background : Black and White

o Button for annotation save

§ If you have a reference block, the reference genome belong to its reference block can be annotated by comparing the other genome.

§ We can obtain the rough annotation information(*.nnt file)

- System