Roadmap

[SilasK]

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]

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]

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]

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

[SilasK]

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]

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]

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 @yinlabniu<https://urldefense.com/v3/__https://github.com/yinlabniu__;!!PvXuogZ4sRB2p-tU!HD_ZAy3E9FK1T96cCVKAT9rDVnXMZ7Ov-wdSeK4PPppCjb7FKHIYG0sHIZ7FnULWyHA1g149Rn9Oxtl9bsSvsQ$> but din't got a reply Maybe you have heard of mmseqs2 which is a tool for fast protein handling. It also implements a sort of HMM profile much faster than HMMER. I would like to create dbcan profiles based on the official dbcan alignments. What do you think? — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/linnabrown/run_dbcan/issues/104*issuecomment-1260479067__;Iw!!PvXuogZ4sRB2p-tU!HD_ZAy3E9FK1T96cCVKAT9rDVnXMZ7Ov-wdSeK4PPppCjb7FKHIYG0sHIZ7FnULWyHA1g149Rn9Oxtkl-VMWPw$>, or unsubscribe<https://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]

Yes thank you very much.