Antônio Camargo

Sure! Let me know if there's anything I can help. Another (minor) consequence of changing the gene caller that I just remembered, and that is somewhat related to an issue...

@ShailNair I think this is due to a incompatibility with the old version of the pipeline and new releases of taxonkit. I just updated the code and uploaded a new...

Hi @LanderDC, Thanks for reporting this! I had forgotten that NCBI stopped updating the FASTA files. I am not in favor of the NR-based solution because it requires downloading the...

@LanderDC yeah, we had a submission to the ICTV challenge using MMseqs2. My only suggestion if you are interested in genus-level classifications is to set a minimum identity to the...

I’ve been exploring UniProt and found the following: - The total number of virus-related proteins in UniProt is much lower than in NCBI. - UniProt’s streaming API has a limit...

I just updated the Zenodo submission with a database generated from NR that I retrieved on 09/02/2024. I'll work on a better pipeline to generate up-to-data databases later on.

@LanderDC, we need to reprocess our submission to the [ICTV Computational Virus Taxonomy Challenge](https://ictv-vbeg.github.io/ICTV-TaxonomyChallenge/). Would you like to be listed as an author? I believe you deserve recognition for raising...

Great! Can you send me your name, affiliation, and ORCID in an email?

@LanderDC I’ve updated the code to translate virus names into species names before verifying their presence in the ICTV taxonomy. This modification enabled the assignment of 6,846,319 (~60.6%) proteins to...

Thank you for the answer, @kenmcd. For some reason, the parenthesis are not working in Affinity, even though they do work with other fonts I tried.