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Seqsphere software v2

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Sourced in Germany

SeqSphere+ software v2.4.0 is a bioinformatics software tool for high-throughput genome sequence analysis. It provides a comprehensive platform for multi-locus sequence typing (MLST) and whole-genome MLST (wgMLST) analysis. The software enables rapid and accurate identification of bacterial strains and facilitates epidemiological investigations.

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2 protocols using seqsphere software v2

1

E. coli MLST Strain Identification

Cited 1 time
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The initial analysis and identification of the strains were performed using an in silico E. coli MLST approach, based on the information available at the E. coli MLST website Enterobase (http://enterobase.warwick.ac.uk/species/index/ecoli) and using Ridom SeqSphere+ software v2.4.0 (Ridom; Münster, Germany) (http://www.ridom.com/seqsphere). Seven housekeeping genes (dnaE, gyrB, recA, dtdS, pntA, pyrC, and tnaA), described previously for E. coli [15 (link)], were used for MLST analysis.
González-Escalona N., Allard M.A., Brown E.W., Sharma S, & Hoffmann M. (2019). Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli. PLoS ONE, 14(7), e0220494.
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2

E. coli MLST Identification Protocol

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The initial analysis and identification of the strains were performed using an in silico E. coli MLST approach, based on the information available at the E. coli MLST website (http://mlst.warwick.ac.uk/mlst/dbs/Ecoli) and using Ridom SeqSphere+ software v2.4.0 (Ridom; Münster, Germany) (http://www.ridom.com/seqsphere). Seven housekeeping genes (dnaE, gyrB, recA, dtdS, pntA, pyrC, and tnaA), described previously for E. coli [36 (link)], were used for MLST analysis. The same E. coli MLST database was also used to assign numbers for alleles and STs.
González-Escalona N, & Kase J.A. (2019). Virulence gene profiles and phylogeny of Shiga toxin-positive Escherichia coli strains isolated from FDA regulated foods during 2010-2017. PLoS ONE, 14(4), e0214620.
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