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linnabrown / run_dbcan

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
http://bcb.unl.edu/dbCAN2
GNU General Public License v3.0
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Roadmap #104

Open SilasK opened 2 years ago

SilasK commented 2 years ago

I just saw that dbCAN get some updates. 

8/9/2022: dbCAN HMMdb v11 is released (based on CAZyDB 8/7/2022). Now the HMMdb contains 699 CAZyme HMMs (452 family HMMs + 3 cellulosome HMMs + 244 subfamily HMMs). The CAZyDB for Diamond search is also updated, containing in total 2,428,817 fasta sequences. See [readme](http://bcb.unl.edu/dbCAN2/download/Databases/dbCAN-old@UGA/readme.txt) for details.
06/29/2022: [dbCAN-sub](https://bcb.unl.edu/dbCAN_sub/) (HMMdb from eCAMI subfams and allows EC and substrate inferences) is now deployed on dbCAN meta server and replaces eCAMI (consumes too much RAM and too slow).

Are there plans to include them in run_dbcan? Would it be difficult to do?

linnabrown commented 2 years ago
  1. dbCAN HMMdb v11 is also updated in our github readme.
  2. dbCAN-sub is a new integrated package in our run_dbcan. We won't update currently here since we will have the formal publication in the future.
linnabrown commented 2 years ago

Also, you suggested that we can let people to download and index the databases when they are installing our bioconda package, I will discuss with @yinlabniu about this and tell you later.

SilasK commented 2 years ago

Do you mean dbCAN-sub is already integrated in your repo?

SilasK commented 2 years ago

I had another Idea. I wrote to @yinlabniu but din't got a reply

Maybe you have heard of mmseqs2 which is a tool for fast protein handling. It also implements a sort of HMM profile much faster than HMMER. I would like to create dbcan profiles based on the official dbcan alignments.

What do you think?

linnabrown commented 2 years ago

Do you mean dbCAN-sub is already integrated in your repo?

dbcan-sub does not integrate with our repo. This software is integrated with the run-dbcan web server.

yinlabniu commented 2 years ago

Thanks, Silas. I believe Lena has answered most of your questions. I've replied via gmail regarding the mmseqs2 profiles.

From: Silas Kieser @.> Sent: Wednesday, September 28, 2022 2:07 AM To: linnabrown/run_dbcan @.> Cc: Yanbin Yin @.>; Mention @.> Subject: Re: [linnabrown/run_dbcan] Roadmap (Issue #104)

Non-NU Email

I had another Idea. I wrote to @yinlabniuhttps://urldefense.com/v3/__https://github.com/yinlabniu__;!!PvXuogZ4sRB2p-tU!HD_ZAy3E9FK1T96cCVKAT9rDVnXMZ7Ov-wdSeK4PPppCjb7FKHIYG0sHIZ7FnULWyHA1g149Rn9Oxtl9bsSvsQ$ but din't got a reply

Maybe you have heard of mmseqs2 which is a tool for fast protein handling. It also implements a sort of HMM profile much faster than HMMER. I would like to create dbcan profiles based on the official dbcan alignments.

What do you think?

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/linnabrown/run_dbcan/issues/104*issuecomment-1260479067__;Iw!!PvXuogZ4sRB2p-tU!HD_ZAy3E9FK1T96cCVKAT9rDVnXMZ7Ov-wdSeK4PPppCjb7FKHIYG0sHIZ7FnULWyHA1g149Rn9Oxtkl-VMWPw$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AEXNKZQPQSGEH7V2B4HDEKLWAPVDLANCNFSM6AAAAAAQTXVXZQ__;!!PvXuogZ4sRB2p-tU!HD_ZAy3E9FK1T96cCVKAT9rDVnXMZ7Ov-wdSeK4PPppCjb7FKHIYG0sHIZ7FnULWyHA1g149Rn9Oxtn6Kz7UKA$. You are receiving this because you were mentioned.Message ID: @.***>

SilasK commented 2 years ago

Yes thank you very much.