DOI: 10.5281/zenodo.13354073
title: EsMeCaTa precomputed database

description: EsMeCaTa precomputed database

Presentation

EsMeCaTa 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 rank
Number of taxa


Species
467


Genus
964


Family
497


Order
277


Class
132


Phylum
89




Each 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.


Usage

The 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_name
taxonomic_affiliation


Cluster_1
Bacteria;Spirochaetes;Spirochaetia;Spirochaetales;Spirochaetaceae;Sphaerochaeta;unknown species


Cluster_2
Bacteria;Chloroflexi;Anaerolineae;Anaerolineales;Anaerolineaceae;ADurb.Bin120;unknown species


Cluster_3
Bacteria;Cloacimonetes;Cloacimonadia;Cloacimonadales;Cloacimonadaceae;Candidatus Cloacimonas;unknown species




Furthermore, 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_folder


This 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 database




Dependencies
Version


UniProt
2024_05


Date
October 2024


NCBI Taxonomy database
2024-10-01


esmecata
0.6.0


mmseqs2
15.6f452


eggnog database
5.0.2


eggnog-mapper
2.1.12


ete3
3.1.3


pandas
2.2.2


biopython
1.84


requests
2.31.0


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.