ORI-GENE Manual

First, your similarity search output files* needs to be converted into ORI-GENE format file with Converter (enclosed in ORI-GENE package). Procedures for the conversion are:

1: Prepare two empty folders (here, termed as gsourceh and gtargeth).

2: Put your similarity search output files into gsourceh folder.

3: Start up Converter.

4: Select search algorithm you used and specify description field length (default=67).

5: Select gsourceh folder location.

6: Select gtargeth folder location.

Converter scans files in gsourceh folder and creates ORI-GENE format files in gtargeth folder. ORI-GENE recognizes these formatted files. To start analysis,

1: Start up ORI-GENE

2: Select "file->New" from menu bar

3: Designate gtargeth folder.

Then, the result will be displayed.

 

ORI-GENE Tools:

ORI-GENE consists of five windows (Tree landscape, Tree explore, Threshold operator, Cluster List, Gene Description browser) and five menus (File, Find, Window, Font, Size).

"Tree landscape viewer" displays an overview of the phylogenetic tree of species, upon which gene distribution patterns are projected. The boxed region in the window is shown at "Tree explore" with enlargement. You can move the target region by Dragging and Dropping the box.

"Tree explorer" As with the NCBI taxonomy Web browser, users can explore the taxonomy by pointing and clicking on selected objects. For example, by clicking on the arrowheads at the branching points of linages, one can "open" (descend) or "close" (ascend) the taxonomy.

"Gene description browser" is an interface enabling one to browse gene descriptions of the homology search output. Within the interface, each description is colored according to its sequence similarity.

"Threshold operator" provides the threshold above which the hit genes are considered for the following analyses. With this interface, users can set the threshold. The selection is immediately reflected by the identification of the origin. The default threshold score is set to 200.

"Cluster list browser" is used for origin-based gene classification. Each line on the list shows the origins and the number of genes classified into respective clusters. Clicking on a line causes a pull down menu to appear showing a list of genes. The distribution patterns can be displayed by selecting a menu item (gene).

*Currently supported formats are: BLAST2, BLAST and FASTA