annotations and allows examination of specific groups. Other
updates include a high-resolution downloadable circular diagram
with direct links between it and the underlying gene pages as well as
an Excel spreadsheet containing all the details on the strength of
the BLAST hit for each of the genes. Researchers can now filter on
the BLAST E-value and the minimum percentage sequence coverage and identity; the results from each are available in the downloadable file for each genome in the comparison.
5.1.13 Protein Family
Sorter
The Protein Family Sorter tool enables researchers to examine the
distribution of specific protein families assigned during annotation
across different genomes. Researchers can select a set (or sets) of
genomes of interest (up to a maximum of 500 genomes) and
examine the distribution of protein families across this set. This
tool first opens showing the pangenome, i.e., all protein families
across all genomes in the selected set. It provides various filtering
options to quickly locate protein families that are conserved across
all the genomes (“core genome”), conserved in only a subset of the
selected genomes (“accessory genome”), or that match a specified
function. A tabular view shows protein families matching the specified filtering criteria, and a recently updated interactive heatmap
viewer provides a graphical bird’s-eye (“pangenome”) view of the
distribution of protein families across the selected genomes. The
heatmap provides clustering and anchoring functions to show relative conservation of synteny and identify lateral transfers.
5.1.14 Comparative
Pathway Viewer
PATRIC’s Comparative Pathway Tool allows researchers to identify
a set of pathways based on taxonomy, EC number, pathway ID,
pathway name, and/or specific annotation type. All pathways at
PATRIC come from the Kyoto Encyclopedia of Genes and Genomes, commonly known as KEGG [141], and the Comparative
Pathway Tool maps the RAST annotations to KEGG pathway
maps. Pathways are classified according to major biological roles
(e.g., carbohydrate metabolism, translation, and biosynthesis of
secondary metabolites) and are assigned identifications from a list
of 137 unique cellular pathways. PATRIC displays a table of unique
pathways that match the search criteria (e.g., the genomes or
proteins chosen by the researcher or at any taxonomic level).
From there, researchers can select specific pathways of interest
and view the Comparative Pathway KEGG Map and the Comparative Pathway Heatmap to compare up to 500 genomes at one time.
5.1.15 Subsystems
PATRIC now computes and displays subsystem data [122] for each
public and privately annotated genome sequence. Subsystems,
which result from manual annotation by a team of expert curators,
are divided into Superclass (e.g., Metabolism), Class (e.g., Stress
Response, Defense, and Virulence), Subclass (e.g., Resistance to
Mycobacterial ID and Characterization Using WGS
439
updates include a high-resolution downloadable circular diagram
with direct links between it and the underlying gene pages as well as
an Excel spreadsheet containing all the details on the strength of
the BLAST hit for each of the genes. Researchers can now filter on
the BLAST E-value and the minimum percentage sequence coverage and identity; the results from each are available in the downloadable file for each genome in the comparison.
5.1.13 Protein Family
Sorter
The Protein Family Sorter tool enables researchers to examine the
distribution of specific protein families assigned during annotation
across different genomes. Researchers can select a set (or sets) of
genomes of interest (up to a maximum of 500 genomes) and
examine the distribution of protein families across this set. This
tool first opens showing the pangenome, i.e., all protein families
across all genomes in the selected set. It provides various filtering
options to quickly locate protein families that are conserved across
all the genomes (“core genome”), conserved in only a subset of the
selected genomes (“accessory genome”), or that match a specified
function. A tabular view shows protein families matching the specified filtering criteria, and a recently updated interactive heatmap
viewer provides a graphical bird’s-eye (“pangenome”) view of the
distribution of protein families across the selected genomes. The
heatmap provides clustering and anchoring functions to show relative conservation of synteny and identify lateral transfers.
5.1.14 Comparative
Pathway Viewer
PATRIC’s Comparative Pathway Tool allows researchers to identify
a set of pathways based on taxonomy, EC number, pathway ID,
pathway name, and/or specific annotation type. All pathways at
PATRIC come from the Kyoto Encyclopedia of Genes and Genomes, commonly known as KEGG [141], and the Comparative
Pathway Tool maps the RAST annotations to KEGG pathway
maps. Pathways are classified according to major biological roles
(e.g., carbohydrate metabolism, translation, and biosynthesis of
secondary metabolites) and are assigned identifications from a list
of 137 unique cellular pathways. PATRIC displays a table of unique
pathways that match the search criteria (e.g., the genomes or
proteins chosen by the researcher or at any taxonomic level).
From there, researchers can select specific pathways of interest
and view the Comparative Pathway KEGG Map and the Comparative Pathway Heatmap to compare up to 500 genomes at one time.
5.1.15 Subsystems
PATRIC now computes and displays subsystem data [122] for each
public and privately annotated genome sequence. Subsystems,
which result from manual annotation by a team of expert curators,
are divided into Superclass (e.g., Metabolism), Class (e.g., Stress
Response, Defense, and Virulence), Subclass (e.g., Resistance to
Mycobacterial ID and Characterization Using WGS
439