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JoanaMPereira / GCsnap

GCsnap: interactive snapshots for the comparison of protein-coding genomic contexts
GNU General Public License v3.0
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Working with proteins not curated in a database #1

Closed naphtap closed 3 years ago

naphtap commented 3 years ago

Hello, I'm trying to start using GCSnap, and the example files worked fine. I have an assembled, annotated genome that has a series of hypothetical proteins I'm interested in examining further. I would like to examine the genomic context of these hypothetical proteins against other organisms. However, my annotated genome hasn't been curated in NCBI yet and I would like to explore the genomic context of the hypothetical proteins further.

Is there a way for me to run GCSnap without needing a database identifier for the hypothetical proteins?

Thanks!

JoanaMPereira commented 3 years ago

Dear Naphtap,

Thanks for reaching out!

In its current version, GCsnap can not deal with user-input assemblies or proteins without a database identifier, but that is definitely in the to-do list.

If your hypothetical proteins have homologs with a database identifier, my suggestion in this case would be to use GCsnap for those and then compare with the context in your assembly...

Thanks a lot for using GCsnap!

Cheers, Joana

naphtap commented 3 years ago

Thanks Joana for your help. I'll go ahead with this! Here's hoping you do make an update to add our own assemblies in the future!