EsMeCaTa precomputed database

EsMeCaTa precomputed databasePresentationEsMeCaTa is a software application to infer consensus proteomes and metabolic functions from taxonomic affiliations. EsMeCaTa uses ete3 and the NCBI Taxonomy database to parse the taxonomic affiliations and query the UniProt Proteomes database to find associated proteomes. These proteomes are clustered using MMseqs2 to create consensus proteomes, which are then annotated with eggNOG-mapper. EsMeCaTa can be time-consuming to run and requires a large number of resources to perform its various steps. A precomputed database has been created to facilitate its use.The EsMeCaTa database has been compiled by taking from UniProt all taxa having at least five proteomes and being of the taxonomic rank of "species", "genus", "family", "order", "class", or "phylum".  EsMeCaTa was applied to these taxa leading to the creation of the database as a zip file.For each taxonomic rank, you can find in the following table the number of taxa that were used by EsMeCaTa to make the predictions:Taxonomic rankNumber of taxaSpecies467Genus964Family497Order277Class132Phylum89Each taxon contained in the database is associated with two files:a protein file in the FASTA format containing the consensus sequences predicted by EsMeCaTa for this taxon.an annotation file resulting from a run of eggNOG-mapper on the consensus sequences.UsageThe precomputed database can be used by EsMeCaTa to make predictions on a tabulated file containing taxonomic affiliations. Two inputs are required:this database.a taxonomic affiliations file in the tsv format looking like this:observation_nametaxonomic_affiliationCluster_1Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Spirochaetaceae;Sphaerochaeta;unknown speciesCluster_2Bacteria;Chloroflexi;Anaerolineae;Anaerolineales;Anaerolineaceae;ADurb.Bin120;unknown speciesCluster_3Bacteria;Cloacimonetes;Cloacimonadia;Cloacimonadales;Cloacimonadaceae;Candidatus Cloacimonas;unknown speciesFurthermore, it is recommended to use the same NCBI Taxonomy database as the one used to create the EsMeCaTa database. This version of the NCBI Taxonomy database is also included in this archive ('taxdmp_2024-10-01.tar.gz'). To use this version of the database, EsMeCaTa relies on the ete3 package to import it with the following command:python3 -c "from ete3 import NCBITaxa; ncbi = NCBITaxa(); ncbi.update_taxonomy_database('taxdmp_2024-10-01.tar.gz')"After these preparatory steps, EsMeCaTa can be called with the following command line:esmecata precomputed -i taxonomic_affiliations.tsv -d esmecata_database.zip -o output_folderThis requires at least EsMaCaTa version 0.5.0. For the information on the output of EsMeCaTa, you can look at the GitHub readme.Dendencies used to create the databaseDependenciesVersionUniProt2024_05DateOctober 2024NCBI Taxonomy database2024-10-01esmecata0.6.0mmseqs215.6f452eggnog database5.0.2eggnog-mapper2.1.12ete33.1.3pandas2.2.2biopython1.84requests2.31.0SPARQLWrapper2.0.0AcknowledgementsMost of the computations presented in this work were performed using the GRICAD infrastructure (https://gricad.univ-grenoble-alpes.fr), which is supported by the Grenoble research community.The work was funded by the ANR project HyLife (ANR-23-CETP-0002) associated with the CETP project HyLife.