-
Notifications
You must be signed in to change notification settings - Fork 21
Home
Rob Edwards edited this page May 8, 2021
·
4 revisions
If you include the --color flag in your PhiSpy.py command, we will color all the genes in the genome (whether or not they are predicted to be in prophages) so you can visualize them in Artemis (see the Artemis PDF manual for more information on Artemis)
The colours we currently use are:
| Color | Meaning |
|---|---|
| Red | This is an integrase or recombinase that likely marks a prophage insertion |
| Blue | This is another phage protein other than integrase |
| Pink | This is a mobile genetic element |
| Light Grey | This is a protein with unknown (hypothetical) function |
| Light Blue | This protein has a hit to your hmm database (note we only colour proteins that are not already red/blue/pink) |