Review





Similar Products

long read whole genome sequencing  (Plasmidsaurus)
86
Plasmidsaurus long read whole genome sequencing
(a) Schematic of the FRφ-encoded shufflon tail fiber protein (TFP) locus, with AlphaFold 3 predictions of each TFP isoform. DNA segments capable of inversion are indicated at the top with circular arrows, and the distinct C-terminal domains are labeled C1–C3; gin encodes the responsible recombinase. (b) Quantification of the relative abundance of each TFP isoform <t>from</t> <t>long-read</t> <t>sequencing</t> of the WT FRφ prophage embedded in the Ent genome, isolated WT phage virions, and a prophage harboring a Δgin deletion mutation. Raw junction counts from HTS reads are listed in white text. (c) Representative plate images after lysogenization assay in a Δgin background, where TFP was locked into each of three distinct states harboring a unique C-terminal domain (C1, C2, or C3). Only phage particles expressing TFP-C2 can lysogenize Ent . (d) Comparison of phage λ lysogenic control locus and FRφ (top), and schematic depictions of cI / cII deletions to generate lytic/virulent FRφ (middle). Superpositions of homologous regions of CI, CII, and Cro are shown for phages λ and FRφ, depicted as AlphaFold 3 predictions, with RMSD values over n α-carbon atoms shown below each structural comparison; superpositions were calculated with the PDBeFold tool from EMBL-EBI. Regions covered by each superposition are indicated on the gene schematics above each predicted structure. (e) Plaquing assay of FRφ mutants ΔcI and ΔcII on a Δprophage strain of Ent , confirming that these mutations produce a lytic phage variant that generates clear zones of cell death. (f) Schematic illustrating the location and type of mutations in sequenced strains that are resistant to infection by FRφ. Three strains contain mutations in fhuA , while two contain mutations in tonB . (g) Plaquing assays demonstrate that FhuA complementation is necessary for FRφ infection in a ΔfhuA knockout strain, shown for both Enterobacter (left) and E. coli (right).
Long Read Whole Genome Sequencing, supplied by Plasmidsaurus, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/long+read+whole+genome+sequencing/sequencing/bio_rxiv__2025__07__22__666180-392-9-15
Average 86 stars, based on 1 article reviews
long read whole genome sequencing - by Bioz Stars, 2026-09
86/100 stars
  Buy from Supplier
hifi long-read whole genome sequencing  (Pacific Biosciences)
90
Pacific Biosciences hifi long-read whole genome sequencing
(a) Schematic of the FRφ-encoded shufflon tail fiber protein (TFP) locus, with AlphaFold 3 predictions of each TFP isoform. DNA segments capable of inversion are indicated at the top with circular arrows, and the distinct C-terminal domains are labeled C1–C3; gin encodes the responsible recombinase. (b) Quantification of the relative abundance of each TFP isoform <t>from</t> <t>long-read</t> <t>sequencing</t> of the WT FRφ prophage embedded in the Ent genome, isolated WT phage virions, and a prophage harboring a Δgin deletion mutation. Raw junction counts from HTS reads are listed in white text. (c) Representative plate images after lysogenization assay in a Δgin background, where TFP was locked into each of three distinct states harboring a unique C-terminal domain (C1, C2, or C3). Only phage particles expressing TFP-C2 can lysogenize Ent . (d) Comparison of phage λ lysogenic control locus and FRφ (top), and schematic depictions of cI / cII deletions to generate lytic/virulent FRφ (middle). Superpositions of homologous regions of CI, CII, and Cro are shown for phages λ and FRφ, depicted as AlphaFold 3 predictions, with RMSD values over n α-carbon atoms shown below each structural comparison; superpositions were calculated with the PDBeFold tool from EMBL-EBI. Regions covered by each superposition are indicated on the gene schematics above each predicted structure. (e) Plaquing assay of FRφ mutants ΔcI and ΔcII on a Δprophage strain of Ent , confirming that these mutations produce a lytic phage variant that generates clear zones of cell death. (f) Schematic illustrating the location and type of mutations in sequenced strains that are resistant to infection by FRφ. Three strains contain mutations in fhuA , while two contain mutations in tonB . (g) Plaquing assays demonstrate that FhuA complementation is necessary for FRφ infection in a ΔfhuA knockout strain, shown for both Enterobacter (left) and E. coli (right).
Hifi Long Read Whole Genome Sequencing, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/long+read+whole+genome+sequencing/long+read+rna+seq+platform+hifi+sequencing/med_rxiv__2025__07__11__25331310-107-41-53
Average 90 stars, based on 1 article reviews
hifi long-read whole genome sequencing - by Bioz Stars, 2026-09
90/100 stars
  Buy from Supplier
whole-genome long-read nanopore sequencing data  (AQUAGEN LTD)
90
AQUAGEN LTD whole-genome long-read nanopore sequencing data
(a) Schematic of the FRφ-encoded shufflon tail fiber protein (TFP) locus, with AlphaFold 3 predictions of each TFP isoform. DNA segments capable of inversion are indicated at the top with circular arrows, and the distinct C-terminal domains are labeled C1–C3; gin encodes the responsible recombinase. (b) Quantification of the relative abundance of each TFP isoform <t>from</t> <t>long-read</t> <t>sequencing</t> of the WT FRφ prophage embedded in the Ent genome, isolated WT phage virions, and a prophage harboring a Δgin deletion mutation. Raw junction counts from HTS reads are listed in white text. (c) Representative plate images after lysogenization assay in a Δgin background, where TFP was locked into each of three distinct states harboring a unique C-terminal domain (C1, C2, or C3). Only phage particles expressing TFP-C2 can lysogenize Ent . (d) Comparison of phage λ lysogenic control locus and FRφ (top), and schematic depictions of cI / cII deletions to generate lytic/virulent FRφ (middle). Superpositions of homologous regions of CI, CII, and Cro are shown for phages λ and FRφ, depicted as AlphaFold 3 predictions, with RMSD values over n α-carbon atoms shown below each structural comparison; superpositions were calculated with the PDBeFold tool from EMBL-EBI. Regions covered by each superposition are indicated on the gene schematics above each predicted structure. (e) Plaquing assay of FRφ mutants ΔcI and ΔcII on a Δprophage strain of Ent , confirming that these mutations produce a lytic phage variant that generates clear zones of cell death. (f) Schematic illustrating the location and type of mutations in sequenced strains that are resistant to infection by FRφ. Three strains contain mutations in fhuA , while two contain mutations in tonB . (g) Plaquing assays demonstrate that FhuA complementation is necessary for FRφ infection in a ΔfhuA knockout strain, shown for both Enterobacter (left) and E. coli (right).
Whole Genome Long Read Nanopore Sequencing Data, supplied by AQUAGEN LTD, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/long+read+whole+genome+sequencing/whole+genome+long+read+nanopore+sequencing+data/pm40646468-246-29-52
Average 90 stars, based on 1 article reviews
whole-genome long-read nanopore sequencing data - by Bioz Stars, 2026-09
90/100 stars
  Buy from Supplier
oxford nanopore long-read whole genome sequencing  (Oxford Nanopore)
90
Oxford Nanopore oxford nanopore long-read whole genome sequencing
(a) Schematic of the FRφ-encoded shufflon tail fiber protein (TFP) locus, with AlphaFold 3 predictions of each TFP isoform. DNA segments capable of inversion are indicated at the top with circular arrows, and the distinct C-terminal domains are labeled C1–C3; gin encodes the responsible recombinase. (b) Quantification of the relative abundance of each TFP isoform <t>from</t> <t>long-read</t> <t>sequencing</t> of the WT FRφ prophage embedded in the Ent genome, isolated WT phage virions, and a prophage harboring a Δgin deletion mutation. Raw junction counts from HTS reads are listed in white text. (c) Representative plate images after lysogenization assay in a Δgin background, where TFP was locked into each of three distinct states harboring a unique C-terminal domain (C1, C2, or C3). Only phage particles expressing TFP-C2 can lysogenize Ent . (d) Comparison of phage λ lysogenic control locus and FRφ (top), and schematic depictions of cI / cII deletions to generate lytic/virulent FRφ (middle). Superpositions of homologous regions of CI, CII, and Cro are shown for phages λ and FRφ, depicted as AlphaFold 3 predictions, with RMSD values over n α-carbon atoms shown below each structural comparison; superpositions were calculated with the PDBeFold tool from EMBL-EBI. Regions covered by each superposition are indicated on the gene schematics above each predicted structure. (e) Plaquing assay of FRφ mutants ΔcI and ΔcII on a Δprophage strain of Ent , confirming that these mutations produce a lytic phage variant that generates clear zones of cell death. (f) Schematic illustrating the location and type of mutations in sequenced strains that are resistant to infection by FRφ. Three strains contain mutations in fhuA , while two contain mutations in tonB . (g) Plaquing assays demonstrate that FhuA complementation is necessary for FRφ infection in a ΔfhuA knockout strain, shown for both Enterobacter (left) and E. coli (right).
Oxford Nanopore Long Read Whole Genome Sequencing, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/long+read+whole+genome+sequencing/oxford+nanopore+sequencing/pm40645177-256-153-148
Average 90 stars, based on 1 article reviews
oxford nanopore long-read whole genome sequencing - by Bioz Stars, 2026-09
90/100 stars
  Buy from Supplier
long-read whole genome sequencing dna  (Oxford Nanopore)
90
Oxford Nanopore long-read whole genome sequencing dna
(a) Schematic of the FRφ-encoded shufflon tail fiber protein (TFP) locus, with AlphaFold 3 predictions of each TFP isoform. DNA segments capable of inversion are indicated at the top with circular arrows, and the distinct C-terminal domains are labeled C1–C3; gin encodes the responsible recombinase. (b) Quantification of the relative abundance of each TFP isoform <t>from</t> <t>long-read</t> <t>sequencing</t> of the WT FRφ prophage embedded in the Ent genome, isolated WT phage virions, and a prophage harboring a Δgin deletion mutation. Raw junction counts from HTS reads are listed in white text. (c) Representative plate images after lysogenization assay in a Δgin background, where TFP was locked into each of three distinct states harboring a unique C-terminal domain (C1, C2, or C3). Only phage particles expressing TFP-C2 can lysogenize Ent . (d) Comparison of phage λ lysogenic control locus and FRφ (top), and schematic depictions of cI / cII deletions to generate lytic/virulent FRφ (middle). Superpositions of homologous regions of CI, CII, and Cro are shown for phages λ and FRφ, depicted as AlphaFold 3 predictions, with RMSD values over n α-carbon atoms shown below each structural comparison; superpositions were calculated with the PDBeFold tool from EMBL-EBI. Regions covered by each superposition are indicated on the gene schematics above each predicted structure. (e) Plaquing assay of FRφ mutants ΔcI and ΔcII on a Δprophage strain of Ent , confirming that these mutations produce a lytic phage variant that generates clear zones of cell death. (f) Schematic illustrating the location and type of mutations in sequenced strains that are resistant to infection by FRφ. Three strains contain mutations in fhuA , while two contain mutations in tonB . (g) Plaquing assays demonstrate that FhuA complementation is necessary for FRφ infection in a ΔfhuA knockout strain, shown for both Enterobacter (left) and E. coli (right).
Long Read Whole Genome Sequencing Dna, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/long+read+whole+genome+sequencing/long+read+whole+genome+sequencing/pm40645177-1017-5-0
Average 90 stars, based on 1 article reviews
long-read whole genome sequencing dna - by Bioz Stars, 2026-09
90/100 stars
  Buy from Supplier
whole genome long-read sequencing  (Oxford Nanopore)
90
Oxford Nanopore whole genome long-read sequencing
(a) Schematic of the FRφ-encoded shufflon tail fiber protein (TFP) locus, with AlphaFold 3 predictions of each TFP isoform. DNA segments capable of inversion are indicated at the top with circular arrows, and the distinct C-terminal domains are labeled C1–C3; gin encodes the responsible recombinase. (b) Quantification of the relative abundance of each TFP isoform <t>from</t> <t>long-read</t> <t>sequencing</t> of the WT FRφ prophage embedded in the Ent genome, isolated WT phage virions, and a prophage harboring a Δgin deletion mutation. Raw junction counts from HTS reads are listed in white text. (c) Representative plate images after lysogenization assay in a Δgin background, where TFP was locked into each of three distinct states harboring a unique C-terminal domain (C1, C2, or C3). Only phage particles expressing TFP-C2 can lysogenize Ent . (d) Comparison of phage λ lysogenic control locus and FRφ (top), and schematic depictions of cI / cII deletions to generate lytic/virulent FRφ (middle). Superpositions of homologous regions of CI, CII, and Cro are shown for phages λ and FRφ, depicted as AlphaFold 3 predictions, with RMSD values over n α-carbon atoms shown below each structural comparison; superpositions were calculated with the PDBeFold tool from EMBL-EBI. Regions covered by each superposition are indicated on the gene schematics above each predicted structure. (e) Plaquing assay of FRφ mutants ΔcI and ΔcII on a Δprophage strain of Ent , confirming that these mutations produce a lytic phage variant that generates clear zones of cell death. (f) Schematic illustrating the location and type of mutations in sequenced strains that are resistant to infection by FRφ. Three strains contain mutations in fhuA , while two contain mutations in tonB . (g) Plaquing assays demonstrate that FhuA complementation is necessary for FRφ infection in a ΔfhuA knockout strain, shown for both Enterobacter (left) and E. coli (right).
Whole Genome Long Read Sequencing, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/long+read+whole+genome+sequencing/long+read+whole+genome+sequencing/pm40546066-8-7-0
Average 90 stars, based on 1 article reviews
whole genome long-read sequencing - by Bioz Stars, 2026-09
90/100 stars
  Buy from Supplier
long-read whole-genome sequencing  (Oxford Nanopore)
90
Oxford Nanopore long-read whole-genome sequencing
(a) Schematic of the FRφ-encoded shufflon tail fiber protein (TFP) locus, with AlphaFold 3 predictions of each TFP isoform. DNA segments capable of inversion are indicated at the top with circular arrows, and the distinct C-terminal domains are labeled C1–C3; gin encodes the responsible recombinase. (b) Quantification of the relative abundance of each TFP isoform <t>from</t> <t>long-read</t> <t>sequencing</t> of the WT FRφ prophage embedded in the Ent genome, isolated WT phage virions, and a prophage harboring a Δgin deletion mutation. Raw junction counts from HTS reads are listed in white text. (c) Representative plate images after lysogenization assay in a Δgin background, where TFP was locked into each of three distinct states harboring a unique C-terminal domain (C1, C2, or C3). Only phage particles expressing TFP-C2 can lysogenize Ent . (d) Comparison of phage λ lysogenic control locus and FRφ (top), and schematic depictions of cI / cII deletions to generate lytic/virulent FRφ (middle). Superpositions of homologous regions of CI, CII, and Cro are shown for phages λ and FRφ, depicted as AlphaFold 3 predictions, with RMSD values over n α-carbon atoms shown below each structural comparison; superpositions were calculated with the PDBeFold tool from EMBL-EBI. Regions covered by each superposition are indicated on the gene schematics above each predicted structure. (e) Plaquing assay of FRφ mutants ΔcI and ΔcII on a Δprophage strain of Ent , confirming that these mutations produce a lytic phage variant that generates clear zones of cell death. (f) Schematic illustrating the location and type of mutations in sequenced strains that are resistant to infection by FRφ. Three strains contain mutations in fhuA , while two contain mutations in tonB . (g) Plaquing assays demonstrate that FhuA complementation is necessary for FRφ infection in a ΔfhuA knockout strain, shown for both Enterobacter (left) and E. coli (right).
Long Read Whole Genome Sequencing, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/long+read+whole+genome+sequencing/long+read+whole+genome+sequencing/pmc12123930-14-12-8
Average 90 stars, based on 1 article reviews
long-read whole-genome sequencing - by Bioz Stars, 2026-09
90/100 stars
  Buy from Supplier
long-read whole genome sequencing  (Pacific Biosciences)
90
Pacific Biosciences long-read whole genome sequencing
Flow chart of isolate inclusion. Number of isolates included in each analysis step and exclusion criteria. In total, 19 MDRB were excluded due to quality exclusion criteria: (i) species mismatched with microbiology report ( n = 1), (ii) contamination check failed ( n = 2), (iii) incomplete <t>sequencing</t> data ( n = 4), and (iv) methylation-related homopolymer errors ( n = 10) or low data quality ( n = 2).
Long Read Whole Genome Sequencing, supplied by Pacific Biosciences, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/long+read+whole+genome+sequencing/genome+sequence/pmc12153326-50-25-21
Average 90 stars, based on 1 article reviews
long-read whole genome sequencing - by Bioz Stars, 2026-09
90/100 stars
  Buy from Supplier
amplicon-based long-read whole genome sequencing (wgs) approach  (Oxford Nanopore)
90
Oxford Nanopore amplicon-based long-read whole genome sequencing (wgs) approach
Flow chart of isolate inclusion. Number of isolates included in each analysis step and exclusion criteria. In total, 19 MDRB were excluded due to quality exclusion criteria: (i) species mismatched with microbiology report ( n = 1), (ii) contamination check failed ( n = 2), (iii) incomplete <t>sequencing</t> data ( n = 4), and (iv) methylation-related homopolymer errors ( n = 10) or low data quality ( n = 2).
Amplicon Based Long Read Whole Genome Sequencing (Wgs) Approach, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/long+read+whole+genome+sequencing/amplicon+sequencing/med_rxiv__2025__05__22__25328149-2-6-15
Average 90 stars, based on 1 article reviews
amplicon-based long-read whole genome sequencing (wgs) approach - by Bioz Stars, 2026-09
90/100 stars
  Buy from Supplier

Image Search Results


(a) Schematic of the FRφ-encoded shufflon tail fiber protein (TFP) locus, with AlphaFold 3 predictions of each TFP isoform. DNA segments capable of inversion are indicated at the top with circular arrows, and the distinct C-terminal domains are labeled C1–C3; gin encodes the responsible recombinase. (b) Quantification of the relative abundance of each TFP isoform from long-read sequencing of the WT FRφ prophage embedded in the Ent genome, isolated WT phage virions, and a prophage harboring a Δgin deletion mutation. Raw junction counts from HTS reads are listed in white text. (c) Representative plate images after lysogenization assay in a Δgin background, where TFP was locked into each of three distinct states harboring a unique C-terminal domain (C1, C2, or C3). Only phage particles expressing TFP-C2 can lysogenize Ent . (d) Comparison of phage λ lysogenic control locus and FRφ (top), and schematic depictions of cI / cII deletions to generate lytic/virulent FRφ (middle). Superpositions of homologous regions of CI, CII, and Cro are shown for phages λ and FRφ, depicted as AlphaFold 3 predictions, with RMSD values over n α-carbon atoms shown below each structural comparison; superpositions were calculated with the PDBeFold tool from EMBL-EBI. Regions covered by each superposition are indicated on the gene schematics above each predicted structure. (e) Plaquing assay of FRφ mutants ΔcI and ΔcII on a Δprophage strain of Ent , confirming that these mutations produce a lytic phage variant that generates clear zones of cell death. (f) Schematic illustrating the location and type of mutations in sequenced strains that are resistant to infection by FRφ. Three strains contain mutations in fhuA , while two contain mutations in tonB . (g) Plaquing assays demonstrate that FhuA complementation is necessary for FRφ infection in a ΔfhuA knockout strain, shown for both Enterobacter (left) and E. coli (right).

Journal: bioRxiv

Article Title: Temperate phages enhance host fitness via RNA-guided flagellar remodeling

doi: 10.1101/2025.07.22.666180

Figure Lengend Snippet: (a) Schematic of the FRφ-encoded shufflon tail fiber protein (TFP) locus, with AlphaFold 3 predictions of each TFP isoform. DNA segments capable of inversion are indicated at the top with circular arrows, and the distinct C-terminal domains are labeled C1–C3; gin encodes the responsible recombinase. (b) Quantification of the relative abundance of each TFP isoform from long-read sequencing of the WT FRφ prophage embedded in the Ent genome, isolated WT phage virions, and a prophage harboring a Δgin deletion mutation. Raw junction counts from HTS reads are listed in white text. (c) Representative plate images after lysogenization assay in a Δgin background, where TFP was locked into each of three distinct states harboring a unique C-terminal domain (C1, C2, or C3). Only phage particles expressing TFP-C2 can lysogenize Ent . (d) Comparison of phage λ lysogenic control locus and FRφ (top), and schematic depictions of cI / cII deletions to generate lytic/virulent FRφ (middle). Superpositions of homologous regions of CI, CII, and Cro are shown for phages λ and FRφ, depicted as AlphaFold 3 predictions, with RMSD values over n α-carbon atoms shown below each structural comparison; superpositions were calculated with the PDBeFold tool from EMBL-EBI. Regions covered by each superposition are indicated on the gene schematics above each predicted structure. (e) Plaquing assay of FRφ mutants ΔcI and ΔcII on a Δprophage strain of Ent , confirming that these mutations produce a lytic phage variant that generates clear zones of cell death. (f) Schematic illustrating the location and type of mutations in sequenced strains that are resistant to infection by FRφ. Three strains contain mutations in fhuA , while two contain mutations in tonB . (g) Plaquing assays demonstrate that FhuA complementation is necessary for FRφ infection in a ΔfhuA knockout strain, shown for both Enterobacter (left) and E. coli (right).

Article Snippet: To identify mutations conferring resistance, cultures were sent for long-read whole genome sequencing (performed by Plasmidsaurus using Oxford Nanopore Technology with custom analysis and annotation).

Techniques: Labeling, Sequencing, Isolation, Mutagenesis, Expressing, Comparison, Control, Variant Assay, Infection, Knock-Out

Flow chart of isolate inclusion. Number of isolates included in each analysis step and exclusion criteria. In total, 19 MDRB were excluded due to quality exclusion criteria: (i) species mismatched with microbiology report ( n = 1), (ii) contamination check failed ( n = 2), (iii) incomplete sequencing data ( n = 4), and (iv) methylation-related homopolymer errors ( n = 10) or low data quality ( n = 2).

Journal: Journal of Clinical Microbiology

Article Title: The dark matter of bacterial genomic surveillance—antimicrobial resistance plasmid transmissions in the hospital setting

doi: 10.1128/jcm.00121-25

Figure Lengend Snippet: Flow chart of isolate inclusion. Number of isolates included in each analysis step and exclusion criteria. In total, 19 MDRB were excluded due to quality exclusion criteria: (i) species mismatched with microbiology report ( n = 1), (ii) contamination check failed ( n = 2), (iii) incomplete sequencing data ( n = 4), and (iv) methylation-related homopolymer errors ( n = 10) or low data quality ( n = 2).

Article Snippet: During an 18-month observation period, 540 clinical gram-negative multidrug-resistant bacterial (MDRB) isolates were collected during routine hospital surveillance and subjected to Pacific Biosciences long-read whole genome sequencing.

Techniques: Sequencing, Methylation