search

JustineCharon / RdRp-scan

Exploring the "dusk matter" of the RNA virosphere
35 stars 5 forks source link

How to run the step 7 motif detection? #2

Open dawnmy opened 1 year ago

dawnmy commented 1 year ago

I have finished to run the first 6 steps. How can I run the step 7: detect A,B,C motifs using RDRP motif database? What output will be generated? Thank you!

yosei-yung commented 1 year ago

Hi, have you already fixed this problem. I also have no idea about how to do the step7. Can you shoule you solution with me? Best, Qingwei

JustineCharon commented 1 year ago

Hi,

Sorry @dawnmy for the delay of my reply ! Motifs can be visualised using sequence editor softwares such as CLC, Geneious etc... You'll need to import the motif fasta file to your editor and use it for detection in your sequences. It has been developped to help with final curation steps rather than preliminary RdRp detections. In case of non divergent RdRp, you can try to run the PalmScan tool to be able to retrieve motif coordinates from high throughput data... Please let me know if you have any further questions ;)

poursalavati commented 1 year ago

Hello, Hope you're doing well. I was wondering about this file that is mentioned in the graphical representation: RdRp-Scan.0.90.RdRp_motifs.geneious

Do you mean separate files in the motif_db folder?

Also are there any motif files for each phyla level (for e.g, Duplornaviricota and etc..)?

Hi,

Sorry @dawnmy for the delay of my reply ! Motifs can be visualised using sequence editor softwares such as CLC, Geneious etc... You'll need to import the motif fasta file to your editor and use it for detection in your sequences. It has been developped to help with final curation steps rather than preliminary RdRp detections. In case of non divergent RdRp, you can try to run the PalmScan tool to be able to retrieve motif coordinates from high throughput data... Please let me know if you have any further questions ;)