A complementary EsMeCaTa precomputed database for phyla with fewer sequenced genomes

Presentation This is a secondary precomputed database of EsMeCaTa for phyla with fewer sequenced genomes. It complements the EsMeCaTa precomputed database. EsMeCaTa's default parameters ignored these phyla. This database has been generated using lower threshold values for esmecata proteomes in order to include these phyla: busco_percentage_keep/--busco to 55 and minimal_number_proteomes/--minimal-nb-proteomes to 3. This repository contains two files: esmecata_database_phyla.zip: zip file containing the files of the precomputed database for the different phyla. It is the file to use with esmecata precomputed command. database_phyla_proteomes_folder.zip: zip file containing several files/folders: scripts to generate input files for esmecata (0_find_phyla_proteomes.py and 1_extract_phyla_poorly_characterised.py). They require the first precomputed database for esmecata (esmecata_database.zip) and generate two files (esmecata_input_phyla.tsv and phylum_uniprot_proteomes.tsv). proteomes_phyla: a folder containing results from esmecata proteomes command with the following parameters: input file esmecata_input_phyla.tsv and with option "--busco 55 --minimal-nb-proteomes 3". Usage Since EsMeCaTa version 0.6.6, it can be used in conjunction of the first precomputed database: esmecata precomputed -i input_file.tsv -o output_folder -d "esmecata_database.zip esmecata_database_phyla.zip" Dendencies used to create the database Dependencies Version UniProt 2025_02 Date May 2025 NCBI Taxonomy database 2025-05-01 esmecata 0.6.5 mmseqs2 15.6f452 eggnog database 5.0.2 eggnog-mapper 2.1.12 ete4 4.3.0 pandas 2.2.2 biopython 1.83 requests 2.32.3 SPARQLWrapper 2.0.0 Acknowledgements Most 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.