Differences between pangenome and panproteome

PanTools offers functionalities to build and analyze a pangenome or panproteome.

A pangenome is constructed from genome and annotation files. First, genome sequences are k-merized and compressed into a De Bruijn graph. Genes and other annotation features from annotation files are integrated into the pangenome as ‘gene’, ‘mRNA’ and ‘CDS’ nodes. Gene start and stop positions are annotated in the graph as relationships and connect the annotation layer to the nucleotide layer. The protein sequences can be clustered into homology groups and connect homologous proteins from different genomes.

A panproteome is built from protein sequences only, ignoring the underlying genome structure. Again, the protein sequences are clustered into homology groups which serve as main input for many functionalities.

In addition to the single layer in panproteomes and three layers in pangenomes, a functional layer can be included in both databases. This layer consists of multiple functional annotation databases (e.g. GO, PFAM) and connects proteins with a shared function.

Since there is only a protein layer and functional layer present in panproteomes, not all functions can be utilized. See the table below for which functions can be used for pangenomes and panproteomes.

Fig. 1 Schematic of genome, annotation, and protein layer of a pangenome database. Figure taken from Efficient inference of homologs in large eukaryotic pan-proteomes

Available functions

Pangenome construction and annotation

Function	Pangenome	Panproteome
build_pangenome	YES	NO
add_genomes	YES	NO
build_panproteome	NO	YES
add_annotations	YES	NO
remove_annotations	YES	NO
add_functions	YES	YES
remove_functions	YES	YES
add_antismash	YES	NO
function_overview	YES	YES
add_phenotype	YES	YES
remove_phenotype	YES	YES
add_variants	YES	NO
remove_variants	YES	NO
add_pavs	YES	YES
remove_pavs	YES	YES
variation_overview	YES	YES
remove_nodes	YES	YES
add_phasing	YES	NO
add_repeats	YES	NO
repeat_overview	YES	NO
group	YES	YES
busco_protein	YES	YES
optimal_grouping	YES	YES
change_grouping	YES	YES
deactivate_grouping	YES	YES
remove grouping	YES	YES
calculate_synteny	YES	NO
add_synteny	YES	NO
synteny_overview	YES	NO

Pangenome analysis

Function	Pangenome	Panproteome
blast	YES	NO
gene_classification	YES	YES
core_unique_thresholds	YES	YES
pangenome_structure	YES	YES
kmer_classification	YES	NO
functional_classification	YES	YES
locate_genes	YES	NO
find_genes_by_name	YES	NO
find_genes_by_annotation	YES	NO
find_genes_in_region	YES	NO
show_go	YES	YES
compare_go	YES	YES
group_info	YES	YES
retrieve_regions	YES	NO
retrieve_features	YES	NO
gene_retention	YES	NO
go_enrichment	YES	YES
order_matrix	YES	YES
rename_matrix	YES	YES
metrics	YES	YES
msa	YES	YES
core_phylogeny	YES	YES
consensus_tree	YES	YES
ani	YES	NO
mlsa_find_genes	YES	NO
mlsa_concatenate	YES	NO
mlsa	YES	NO
edit_phylogeny	YES	YES
root_phylogeny	YES	YES
create_tree_template	YES	YES
map	YES	NO
sequence_visualization	YES	NO
calculate_dn_ds	YES	NO