SEA-PHAGES | GeneMarkS ?

Link to this post \| posted 26 Jan, 2021 00:49
JPeterGo	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 267Kb

Link to this post | 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

Link to this post \| posted 26 Jan, 2021 00:57
debbie	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. debbie Edited 26 Jan, 2021 00:58

Link to this post \| posted 05 Apr, 2024 01:02
catadav	Hello! 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 http://exon.gatech.edu/GeneMark/gm.cgi but I also got an error message. Is this happening to anyone else?

Link to this post | posted 05 Apr, 2024 01:02

catadav

Hello!

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 http://exon.gatech.edu/GeneMark/gm.cgi but I also got an error message. Is this happening to anyone else?

Link to this post \| posted 05 Apr, 2024 18:14
debbie	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: https://seaphagesbioinformatics.helpdocsonline.com/article-68 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. Best, debbie

Link to this post | posted 05 Apr, 2024 18:14

debbie

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:
https://seaphagesbioinformatics.helpdocsonline.com/article-68
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.

Best,
debbie

Link to this post \| posted 06 Apr, 2024 22:47
catadav	Thank you Debbie! I could run the web-based GeneMark S and uploaded it to PECAAN.

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