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Associated diseases

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SpeciesFinder specifications


Unique identifier OMICS_10774
Name SpeciesFinder
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.2
Stability Stable
Maintained Yes


  • person_outline SpeciesFinder <>

SpeciesFinder in publications

PMCID: 5764278
PMID: 29324839
DOI: 10.1371/journal.pone.0190647

[…] specific for c. coli, c. jejuni, c. lari and c. upsaliensis [], revealed the highest match of 87% with c. lari ( and ). because of this relatively low similarity, strain 12 was also typed with the speciesfinder 1.2 service at the center for genomic epidemiology website (https://cge.cbs.dtu.dk/services/speciesfinder/). the outcome was again c. lari (data not shown). for six isolates new alleles […]

PMCID: 5722073
PMID: 29192087
DOI: 10.1128/genomeA.01381-17

[…] short palindromic repeat (crispr) arrays on nodes/contigs 30, 50, and 116 in the genome., st-18:k073 was confirmed as an e.¬†faecium strain with the 16s rrna-based species identification tool, speciesfinder (v1.2) (). st-18:k073 was similar to other e.¬†faecium draft genomes, including strains k60-39 (genbank accession no. cp023423), do (cp003583), a_020709_82 (cp018128), and e745 […]

PMCID: 5051641
PMID: 27493201
DOI: 10.1242/bio.017673

[…] with using the v3-600 cycle kit (illumina). whole genome sequences were then assembled using lasergene software (dnastar)., for each sequencing project, we confirmed the individual species with the speciesfinder 1.2 algorithm () and calculated genome to genome distances with the genome to genome distance calculator of the leibniz institute dsmz-german collection of microorganisms and cell […]

PMCID: 4844618
PMID: 27199912
DOI: 10.3389/fmicb.2016.00576

[…] genome automatic annotation pipeline (pgaap) ()., for all the five wgs-sequences, species were confirmed by using the strain identification tool (eztaxon server) and/or the species finder tool (speciesfinder 1.0) using annotated full length 16s rrna sequences and/or assembled contigs as input, respectively (). besides, all five wgs-sequences were analyzed for mlst allelic profile, st type […]

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SpeciesFinder institution(s)
Center for Genomic Epidemiology, DTU, Kemitorvet, Kgs Lyngby, Denmark
SpeciesFinder funding source(s)
The Danish Council for Strategic Research

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