The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

Welcome to the forums at Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at

GeneMarkS ?

| posted 26 Jan, 2021 00:49
The manual says to use the host trained Genemark version. The phage we are working with has a pretty large genome (192kB), and the coding potential from genemarkS looks crisper than the host trained one. (And for some of the genes host trained Genemark shows no coding potential, whereas genemarkS gives rather convincing curves.
Does anything speak against using the phage trained genemarkS output in PECAAN?
Johann Peter Gogarten
Edited 26 Jan, 2021 00:49
| posted 26 Jan, 2021 00:57
Hi. I typically use the phage trained GeneMark in PECAAN, so no harm. Be sure to label the file so you know which one it is. BUT I use the host(s) trained outside of PECAAN because all can be informative, especially in the difficult to call areas.
Edited 26 Jan, 2021 00:58
| posted 05 Apr, 2024 01:02

Is GeneMark down? I have been trying to run genemark S and the host trained Genemark for several phages but I always get the following message:

"Can't connect to GeneMark
We could not connect to the GeneMark servers. If this error persists, please contact us".

I also tried to run the online version in but I also got an error message. Is this happening to anyone else?
| posted 05 Apr, 2024 18:14
Hi all,
It does look like parts of GeneMark is down. I have written to their administrator to help to resolve.
In the meantime, at least when I try, the Gene Mark server is working for GeneMark S. You can follow the direction from the guide found here:
I think you can make all of the selections found in the guide except, the RBS model choice is no longer available.

As for GeneMark host trained data, we will need to wait on the website for more information. i will continue to follow up.

| posted 06 Apr, 2024 22:47
Thank you Debbie!

I could run the web-based GeneMark S and uploaded it to PECAAN.
| posted 21 May, 2024 17:30

GeneMark is down on PhagesDB. So I tried to follow the instructions listed above to run GeneMarkS online. That didn't work for me. Please see attached for the error message I got.

Has anyone got GeneMarkS to run today?

| posted 21 May, 2024 21:34
I can verify that it is down. If it isn't back by tomorrow, i will contact the folks at GeneMark.
| posted 22 May, 2024 15:30
Both GeneMarkS and host trained GeneMark are back online through PhagesDB!
Login to post a reply.