Open SevanEsaian opened 4 months ago
Thank you for using our tool. You can use cgc_standard.out to do that
https://dbcan.readthedocs.io/en/latest/search.html?q=cgc_standard.out
Thank you for the suggestion. I will take a look at your link. If I have follow-up questions, I will contact you again in this thread.
Thank you for the suggestion. I will take a look at your link. If I have follow-up questions, I will contact you again in this thread.
Hi.
In the dbCAN3, we have the result of CAZyme and also, the cgc.gff, which is the result of CGCFinder. I just tested and if you could import the cgc.gff into Geneious, it would show you the visualization result (Attached file).
In our dbCAN-seq and dbCAN3 paper, we define that the CGC(CAZyme gene cluster) is the computational PULs, which include CAZyme, TC, TF, and STP (https://academic.oup.com/nar/article/51/W1/W115/7147496).
Hope this will help you. If needed we could try to generate the prokka-style output for CAZymes and CGCs in the future.
Please let me if you need anything else, or you could give us your example file to show.
Best,
Do you still have question? @SevanEsaian
Hello,
I am working on identifying potential PULs in my metagenomes. I've run my dereplicated bins through prokka and dbCAN. I have uploaded the fasta file and prokka annotation to Geneious which overlap nicely. However, the dbCAN output file does not match the output structure of prokka; such that, I can't see the CAZyme annotation. Instead, it just says "CDS".
My question is: do you have suggestion for where I can find a script that organizes the dbcan .gff output file; such that, I can see the corresponding CAZyme on Geneious alongside my .fasta file?
Thank you.