[Request] MSA input option in LOMETS2 server

Dear Zhang lab,

I would like to suggest/request that you add the option to input a user-generated MSA in the LOMETS2 server (it would, of course, also be useful in many of your other servers - explanation below).

Your new DeepMSA pipeline is well thought out, however it prevents users from including non-redundant sequences absent from UniProt (UniClust/UniRef) and Metaclust.

To clarify:

1. There are currently many genome assemblies whose predicted proteome is not yet included in any major public database (UniProt or NCBI). These proteomes are only available in specialized genomic databases (e.g. TriTrypDB for kinetoplastids), lab group websites and/or data repositories like Dryad.

2. Likewise, there are thousands of published transcriptome assemblies whose predicted protein sequences are, again, made available only in specific databases or data repositories, outside the realm of UniProt or NCBI. Particularly important examples include the Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) and the 1000 Plants Project (1kP). Transcriptome datasets are all the more relevant because in many cases, particularly for protist species without a sequenced genome, they are our only window into a given species proteome.

3. Metaclust is great, but unfortunately misses other metagenomics/metatranscriptomics datasets, like the ones included in the Soil Reference Catalog (SRC) and Marine Eukaryotic Reference Catalog (MERC), also generated in Söding's lab.

Rich, manually curated MSAs that include sequences from all available sources, as detailed above, have the potential to be much more informative for LOMETS (and other servers from your lab) than the ones DeepMSA is currently able to generate.

This is a particularly important consideration when working with proteins from evolutionary lineages that on top of being very divergent, also do not contain many species with genome annotations in UniProt or NCBI. This is the case with kinetoplastids, which I do research on, as well as several other protist lineages.

I hope you see my suggestion/request on a positive light and can implement it soon. Let me know your thoughts.

Cheers,
Jose