How to visualize the prophages?
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#1 How to visualize the prophages?
I'm trying to make a diagram exactly like the one on page 6 of the manual, v. 0.95. I have 5 genomes and a mulit-fasta file of phage sequences. I've attached what I have so far. One thing that's puzzling me is that when I go to \\\"add custom features\\\" and select my phage ring I do not see "multi fasta" as an option. What am I doing wrong? Thanks again.
Have you specified a gap between entries in the
multi-fasta file (if theres no spacer between entries, then there's no
gap to load). Please see the attached screenshot.
Hmm. I'm not seeing a Spacer field, screenshot attached.
No! My mistake. I see you use the prophage file as a reference, I was using a genome seq. as reference, which was not multi-fasta. Now I see Spacer, my bad.
OK, clearly my understanding is incomplete. In order to make Figure 3 in the manual how did you make the outermost ring, with the prophage sequences? Does this rely on custom features or does this use BRIG's blast analysis? If it's using custom features then what was the input file? Thanks again.
oh. The prophage annotations in figure three were derived from annotation in a genbank file.
This image shows the genome of E. coli O157:H7 Sakai as the reference, the genbank file I have for this genome has the prophage regions marked as "misc_features" so it was a matter of loading in these annotations from the genbank file into BRIG, please see section 8 in particular page 41 in the manual.
Annotations can also be loaded from a table as well, which is also in section 8 of the manual.
apologies for any confusion.