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target definer tool within ridom seqsphere+ software version 8  (Ridom GmbH)

 
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    Ridom GmbH target definer tool within ridom seqsphere+ software version 8
    Target Definer Tool Within Ridom Seqsphere+ Software Version 8, supplied by Ridom GmbH, 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/seqsphere++software/target+definer+tool+within+ridom+seqsphere++software+version+8/pm40570713-94-23-27
    Average 90 stars, based on 1 article reviews
    target definer tool within ridom seqsphere+ software version 8 - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    Sequencing:

    Article Title: Core genome multilocus sequence typing (cgMLST) indicates herd specificity of Fusobacterium necrophorum ssp. necrophorum isolated from dairy cattle interdigital phlegmon outbreaks in Finland.
    Article Snippet: The raw reads were trimmed using Local Run Manager tools on MiSeq and assembled with Velvet software version 1.1.04. .. An ad hoc gene-by-gene analysis schema was created based on the nucleotide sequence of the complete FNN genome available from GenBank, utilizing the Target Definer tool within Ridom SeqSphere+ software version 8 (Ridom, Germany). .. Sequence of NZ_CP034842.1 (FNN, ATCC 25286) was used as a seed genome and NZ_CP033837.1 (Fusobacterium necrophorum strain FDAARGOS_565) was added as a penetration query genome.

    Software:

    Article Title: Core genome multilocus sequence typing (cgMLST) indicates herd specificity of Fusobacterium necrophorum ssp. necrophorum isolated from dairy cattle interdigital phlegmon outbreaks in Finland.
    Article Snippet: The raw reads were trimmed using Local Run Manager tools on MiSeq and assembled with Velvet software version 1.1.04. .. An ad hoc gene-by-gene analysis schema was created based on the nucleotide sequence of the complete FNN genome available from GenBank, utilizing the Target Definer tool within Ridom SeqSphere+ software version 8 (Ridom, Germany). .. Sequence of NZ_CP034842.1 (FNN, ATCC 25286) was used as a seed genome and NZ_CP033837.1 (Fusobacterium necrophorum strain FDAARGOS_565) was added as a penetration query genome.



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    Population structure of the global Rhodococcus equi dataset including 233 genomes from 18 countries. Tree constructed using ad hoc core-genome MLST (cgMLST) scheme containing 2’737 genes generated in Ridom Seqsphere + v9.0.1 ( https://www.ridom.de/seqsphere/cgmlst/ ) and converted to a neighbor-joining phylogeny using the R package ape . The cgMLST phylogeny was rooted at the mid-point and visualized using iTOL . The year and country of isolation are shown in the inner and second ring from the centre respectively. Source attribution of the different isolates is shown in the third ring. Presence/absence of the virulence-associated plasmid and the various plasmid categories are color-coded in the outer ring. The scale bar expresses the average number of nucleotide substitutions per site

    Journal: BMC Microbiology

    Article Title: Multi-host distribution of Rhodococcus equi (Prescottella equi) strains and their phylogenomic clustering

    doi: 10.1186/s12866-025-04152-8

    Figure Lengend Snippet: Population structure of the global Rhodococcus equi dataset including 233 genomes from 18 countries. Tree constructed using ad hoc core-genome MLST (cgMLST) scheme containing 2’737 genes generated in Ridom Seqsphere + v9.0.1 ( https://www.ridom.de/seqsphere/cgmlst/ ) and converted to a neighbor-joining phylogeny using the R package ape . The cgMLST phylogeny was rooted at the mid-point and visualized using iTOL . The year and country of isolation are shown in the inner and second ring from the centre respectively. Source attribution of the different isolates is shown in the third ring. Presence/absence of the virulence-associated plasmid and the various plasmid categories are color-coded in the outer ring. The scale bar expresses the average number of nucleotide substitutions per site

    Article Snippet: Core-genome MLST (cgMLST) analysis for 286 R. equi genomes was performed in Ridom Seqsphere+ (v9.0.1; Ridom GmbH, Münster, Germany).

    Techniques: Construct, Generated, Isolation, Plasmid Preparation