Genome Analysis Software Info Site

How to load GBFF file into IMC.

The GBFF file is a compressed file containing a large number of GenBank format files and consists of two files.

One has a file extension "*. gbff.gz" in the definition file (eg bacteria.1002.genomic.gbff.gz).

The other has a file extension "*. fna.gz" in the sequence file (eg bacteria.1002.1.genomic.fna.gz).

Operation

1. Save the above two files in an arbitrary place.
2. From the menu, click "Tools -> Multi GenBank File Expander ...".
3. 
4. The "Expand Setting" dialog is displayed.
5. 
6. For "Multi GenBank Format File" text field,  click "Ref ..." to specify the saved "*. gbff.gz" file.
7. For "fna File" text field, click "Ref ..." to specify the saved "*. fna.gz" file.
8. For "Expand Directory" text field, specify the directory where you want to expand the GBFF file.
9. 
10. Click "Run".
11. A confirmation message "Start Expand?" is displayed.
12. 
13. Click "Yes".
14. Execution starts, and a progress message is displayed during execution.
15. 
16. When the progress message is closed, expansion is completed.
17. Following taxonomy below the directory specified for expansion, it is expanded hierarchically.
18. 

Loading to the IMC is as follows.

1. Right-click on the main directory tree root.
2. The menu will be displayed.
3. 
4. Click "Change Root Directory ...".
5. A confirmation message "Change Root Diretory?" is displayed.
6. 
7. Click "Yes".
8. The file selection dialog is displayed.
9. Specify the directory where you previously specified expansion.
10. 
11. The expanded directory is changed to the root directory.
12. 
13. Click + mark to expand the tree manually.
14. 
15. When the sequence node is displayed, click on one "*. gbk" file.
16. A confirmation message "Change Current Directory?" is displayed.
17. 
18. If the directory to which the sequence belongs contains a very large number of files, loading takes time.
19. In such a case, it is recommended to manually split the directory.
20.  
21. Click "Yes".
22. The directory containing the sequence becomes the current directory and all files belonging to it are loaded.
23. While loading, a progress message will be displayed.
24. 
25. The clicked gbk file becomes the current file and it is displayed in the main feature map.
26.