Article Figures & Data
Figures
- FIG 1
Schematic of all genomic, bioinformatic, and scripting workflows used to create FusoPortal.
- FIG 2
Correction of open reading frames in Fusobacterium genomes. (A) A comparison of the genome size to the number of protein-encoding genes per genome in both the NCBI and FusoPortal genomes. (B) A comparison of all proteins for average gene size in the NCBI and FusoPortal genomes. (C) Analysis of all proteins 1,000 residues in size and above in annotated FusoPortal proteomes and of how many residues were added (or, in rare cases, removed) compared to the previous annotations present in the NCBI database. n = number of proteins 1,000 residues in size or greater in each genome.
- FIG 3
Phylogenetic analysis of complete Fusobacterium genomes. (A) Tree created using complete proteomes in the microPan package in R. Bootstrap values are indicated in red. Locations of where strains were isolated in the human body are highlighted. (B) Micropan analysis of pan-genome gene families with models predicting the percentages of core genes, shell genes (present in most genomes), and cloud genes (found in few genomes). (C) Analysis of the number of unique gene clusters found among the eight complete FusoPortal genomes.
- FIG 4
Navigating the FusoPortal Web interface for genome analysis. (A) Links are provided for downloading all genomic data (raw and analyzed), with Bandage plots to show the completeness of each genome build. (B) Whole-genome maps were produced with links to custom webpages for each gene that provide access to all genomic and bioinformatic analysis. (C) Each gene contains a full InterPro analysis page with links to multiple functional prediction databases (e.g., PFAM, TIGR, Gene3D, CDD, GO). No IPR, no InterPro accession number.
- FIG 5
A custom BLAST database to search FusoPortal genomes built with SequenceServer. (A) Data entry panel that autodetects protein or DNA sequences. (B) The available genomes that users can choose to search. (C) BLAST results for identified genes. (D) Links to downloadable files.
Tables
- TABLE 1
Statistics and NCBI accession numbers for FusoPortal genomes
Species Strain NCBI GenBank
sequence
accession no.No. of NCBI
contigsaSize
(Mb)No. of
protein
genesFusoPortal GenBank
sequence
accession no.No. of
FusoPortal
contigsSize
(Mb)No. of
protein
genesF. nucleatum 23726 GCF_000178895.1 67 2.23 1,983 GCA_003019785.1 1 2.30 2,111 F. nucleatum 25586 GCA_000007325.1 1 2.17 1,968 GCA_003019295.1 1 2.18 2,019 F. varium 27725 GCA_000159915.2 39 3.30 3,008 GCA_003019655.1 1 3.35 3,054b F. ulcerans 49185 GCA_000158315.2 49 3.49 3,191 GCA_003019675.1 1 3.54 3,230 F. mortiferum 9817 GCA_000158195.2 44 2.67 2,538 GCA_003019315.1 1 2.72 2,631 F. gonidiaformans 25563 GCA_000158835.2 24 1.70 1,618 GCA_003019695.1 1 1.68 1,617 F. periodonticum 2_1_31 GCA_000158215.3 61 2.55 2,375 GCA_003019755.1 1 2.54 2,388 F. necrophorum 1_1_36S GCA_000242215.1 40 2.31 3,197 GCA_003019715.1 1 2.29 21,215 ↵a Contig, continuous stretch of genomic DNA with breaks.
↵b Data include 70 genes from a 42-kb plasmid (GCA_003019655.1).
