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target definer tool in ridom seqsphere+ software  (Ridom GmbH)

 
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    Ridom GmbH target definer tool in ridom seqsphere+ software
    Target Definer Tool In Ridom Seqsphere+ Software, 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/seqsphere++target+definer+tool/pm40633272-114-13-13
    Average 90 stars, based on 1 article reviews
    target definer tool in ridom seqsphere+ software - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    Software:

    Article Title: Genomic epidemiology of avian pathogenic Escherichia coli in two broiler colibacillosis outbreaks in Finland.
    Article Snippet: .. The scheme for gene-by-gene analysis was defined using the Target Definer tool in Ridom SeqSphere+ software (Münster, Germany). ..

    Article Title: Salmonella Typhimurium outbreak associated with frozen tomato cubes at a restaurant in western Finland, January to February 2021
    Article Snippet: Multilocus sequence typing (MLST) and cluster analysis (cgMLST) from sequence data were done using Ridom SeqSphere+ [9-11]. .. Briefly, we used the Ridom SeqSphere+ software’s Target Definer tool with default parameters to identify 3,696 targets defined for cgMLST shared by the Salmonella Reference Genome NC_011294.1 (Salmonella enterica subsp. enterica serovar Enteritidis str. ..

    other:

    Article Title: Association of Phylogenomic Relatedness among Neisseria gonorrhoeae Strains with Antimicrobial Resistance, Austria, 2016–2020
    Article Snippet: We generated a local N. gonorrhoeae core-genome multilocus sequence typing (cgMLST) scheme with SeqSphere+ target definer tool version 6.0.0 (Ridom, ttps:// www.ridom.de ) ( ) ( ).

    Article Title: Bacterial contamination of water used as thermal transfer fluid in fluid-warming devices.
    Article Snippet: Core-genome multi-locus sequence typing A M. chimaera core-genome multi-locus sequence typing (cgMLST) scheme was generated with the SeqSphereþ Target Definer Tool Version 6.0.0 (Ridom Inc., Muenster, Germany) in accordance with the manufacturer’s instructions.

    Article Title: Rifampicin Resistance Associated with rpoB Mutations in Neisseria gonorrhoeae Clinical Strains Isolated in Austria, 2016 to 2020
    Article Snippet: A local N. gonorrhoeae core genome MLST (cgMLST) scheme was generated with the SeqSphere+ target definer tool (version 6.0.0; Ridom, Muenster, Germany) ( ) using strain MS11 as a seed genome (NCBI accession number NC_022240.1 ) and 47 complete N. gonorrhoeae genomes as query sequences (accession numbers NC_002946.2 , NC_011035.1 , NZ_CP012026.1 , NZ_CP012027.1 , NZ_CP012028.1 , NZ_CP016015.1 , NZ_CP016016.1 , NZ_CP016017.1 , ABZF00000000.1 , ABZG00000000.1 , ABZH00000000.1 , ACIG00000000.1 , ADAA00000000.1 , ABZJ00000000.2 , ABZI00000000.1 , ABZM00000000.1 , ABZL00000000.1 , ABZN00000000.1 , ABZO00000000.1 , ABZP00000000.1 , ABZQ00000000.1 , CQLK00000000.1 , CQJM00000000.1 , CQME00000000.1 , CQJI00000000.1 , CQIM00000000.1 , CQHK00000000.1 , CQLD00000000.1 , CQNW00000000.1 , CQKW00000000.1 , CQJY00000000.1 , CQIY00000000.1 , CQJB00000000.1 , CQKU00000000.1 , CQOV00000000.1 , CQIR00000000.1 , CQJZ00000000.1 , CQKM00000000.1 , CQMI00000000.1 , CQMT00000000.1 , CQKB00000000.1 , CQOT00000000.1 , CQJD00000000.1 , CHZN00000000.1 , CFRU00000000.1 , AKCG00000000.1 , and AKCH00000000.1 ) and applying default software parameters.

    Article Title: Genetic diversity and known virulence genes in Listeria innocua strains isolated from cattle abortions and farm environment
    Article Snippet: Ad hoc cgMLST scheme with 1347 loci covering 35% of L. innocua genome was developed using Ridom SeqSphere+ target definer.

    Article Title: Association of Phylogenomic Relatedness among Neisseria gonorrhoeae Strains with Antimicrobial Resistance, Austria, 2016–2020
    Article Snippet: A local N. gonorrhoeae cgMLST scheme was generated with SeqSphere+ target definer tool (version 6.0.0, Ridom, Münster, Germany) (3).



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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