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raw-lab / MetaCerberus

Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focus of shotgun metaomics data
BSD 3-Clause "New" or "Revised" License
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Could you add the NCyc database to MetaCerberus? #23

Open ywangbioinfo opened 4 months ago

ywangbioinfo commented 4 months ago

Thank for your great work.

I have tried MetaCerberus in my linux OS, it is fine. Now I am going to annotate a genome, and will search for some denitrification genes. If MetaCerberus could integrate the NCyc database, it will be nice to me.

NCyc：a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes https://github.com/qichao1984/NCyc

raw-lab commented 1 month ago

Good afternoon,

COG, KEGG, FOAMdb (especially should cover these) genes. Is there a particular set of genes you are looking for? We are working on updating FOAMdb 2.0 to cover the genes that were in NCyc.

Also, if you have your own HMMs and metadata you should be able to do a custom database with MetaCerberus. We give instructions in the README for this.

Closing for now.

Let us know if you need a hand?

many thanks, RAW Lab

ywangbioinfo commented 1 month ago

Hi,

Thank you for your response. I am searching for denitrification genes like nirS/nirK. Since your new FOAM database will cover them, I think it is sufficient for me. Again, thanks for your great work.

2024年10月9日(水) 0:33 RAW Lab @.***>:

Good afternoon,

COG, KEGG, FOAMdb (especially should cover these) genes. Is there a particular set of genes you are looking for? We are working on updating FOAMdb 2.0 to cover the genes that were in NCyc.

Also, if you have your own HMMs and metadata you should be able to do a custom database with MetaCerberus. We give instructions in the README for this.

Closing for now.

Let us know if you need a hand?

many thanks, RAW Lab

— Reply to this email directly, view it on GitHub https://github.com/raw-lab/MetaCerberus/issues/23#issuecomment-2400181325, or unsubscribe https://github.com/notifications/unsubscribe-auth/AVDBXR6XDE6JYJE722DGAD3Z2P3NFAVCNFSM6AAAAABLNTJXX2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMBQGE4DCMZSGU . You are receiving this because you authored the thread.Message ID: @.***>

raw-lab commented 1 month ago

We just made custom HMMs for nirK and nirS for a collaborator. Do you want nosZ as well? I can send you the links.

raw-lab commented 1 month ago

We have just made those HMMs do you want them?

ywangbioinfo commented 1 month ago

Thank you for your quick response. I would like to receive the HMMs of nirS, nirK, and nosZ genes.