5.1.7 Similar Genome
Finder Service
When a researcher has a new genome sequence, one of the first
things they want to identify is the closest relatives of their genome.
PATRIC provides a new service that allows researchers to do this
using Mash/MinHash [130]. Mash reduces large sequences and
sequence sets to small representative sketches, which can be used to
estimate mutation distances based on shared k-mers. The MinHash
dimensionality-reduction technique to include a pairwise mutation
distance and p-value significance test enables the efficient clustering
and search of massive sequence collections. The results are returned
as a list of the most similar genome sequences with corresponding
metadata.
5.1.8 Genome Alignment
In November 2018, PATRIC launched the Genome Alignment
Service to enable users to compute whole-genome sequence alignments. This service uses progressiveMauve [131], which constructs
positional homology multiple genome sequence alignments for up
to twenty genome sequences. The output of the service includes a
visual display of the genome that allows users to view and explore
the entire genome sequence alignment or to zoom in to compare
individual regions or genes.
5.1.9 Codon Trees
A phylogenetic tree (or evolutionary tree) is a branching diagram or
“tree” showing the evolutionary relationships among various
biological species or other entities. The Codon Tree service in
PATRIC allows researchers to build trees that contain private and
public genomes, adjusting for the number of genes that will be used
to generate the tree. The service uses a defined number of
sequences picked randomly from PATRIC’s global Protein Families
(PGFams) [124] to build an alignment. A tree based on the differences between the selected sequences is then generated. Protein
sequences are aligned using MUSCLE [132], and the nucleotide
coding gene sequences are aligned using the Codon_align function
of BioPython [133]. A concatenated alignment of all proteins and
nucleotides is written to a PHYLIP formatted file, and then a
partition file for RaxML [134] is generated. Support values are
generated using 100 rounds of the “Rapid” bootstrapping option
[135] of RaxML.
In addition to the Newick-formatted tree files, the service
returns a portable document format (PDF) file, a portable network
graphics (PNG), and a scalable vector graphics (SVG) image file of
the midpoint rooted tree images generated by FigTree (http://tree.
bio.ed.ac.uk/software/figtree/). The phylogenetic tree view on
the PATRIC website allows researchers to select nodes and leaves,
enabling the user to create groups from specific clades for further
analysis. It also generates a genome report that provides a list of the
genome sequences and protein families used in the construction of
the tree and the counts of genes, proteins, amino acids, and
Mycobacterial ID and Characterization Using WGS
437
Finder Service
When a researcher has a new genome sequence, one of the first
things they want to identify is the closest relatives of their genome.
PATRIC provides a new service that allows researchers to do this
using Mash/MinHash [130]. Mash reduces large sequences and
sequence sets to small representative sketches, which can be used to
estimate mutation distances based on shared k-mers. The MinHash
dimensionality-reduction technique to include a pairwise mutation
distance and p-value significance test enables the efficient clustering
and search of massive sequence collections. The results are returned
as a list of the most similar genome sequences with corresponding
metadata.
5.1.8 Genome Alignment
In November 2018, PATRIC launched the Genome Alignment
Service to enable users to compute whole-genome sequence alignments. This service uses progressiveMauve [131], which constructs
positional homology multiple genome sequence alignments for up
to twenty genome sequences. The output of the service includes a
visual display of the genome that allows users to view and explore
the entire genome sequence alignment or to zoom in to compare
individual regions or genes.
5.1.9 Codon Trees
A phylogenetic tree (or evolutionary tree) is a branching diagram or
“tree” showing the evolutionary relationships among various
biological species or other entities. The Codon Tree service in
PATRIC allows researchers to build trees that contain private and
public genomes, adjusting for the number of genes that will be used
to generate the tree. The service uses a defined number of
sequences picked randomly from PATRIC’s global Protein Families
(PGFams) [124] to build an alignment. A tree based on the differences between the selected sequences is then generated. Protein
sequences are aligned using MUSCLE [132], and the nucleotide
coding gene sequences are aligned using the Codon_align function
of BioPython [133]. A concatenated alignment of all proteins and
nucleotides is written to a PHYLIP formatted file, and then a
partition file for RaxML [134] is generated. Support values are
generated using 100 rounds of the “Rapid” bootstrapping option
[135] of RaxML.
In addition to the Newick-formatted tree files, the service
returns a portable document format (PDF) file, a portable network
graphics (PNG), and a scalable vector graphics (SVG) image file of
the midpoint rooted tree images generated by FigTree (http://tree.
bio.ed.ac.uk/software/figtree/). The phylogenetic tree view on
the PATRIC website allows researchers to select nodes and leaves,
enabling the user to create groups from specific clades for further
analysis. It also generates a genome report that provides a list of the
genome sequences and protein families used in the construction of
the tree and the counts of genes, proteins, amino acids, and
Mycobacterial ID and Characterization Using WGS
437