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probeCheck specifications

Information


Unique identifier OMICS_09181
Name probeCheck
Interface Web user interface
Restrictions to use None
Input data One or more sequences in FASTA format into the textfield or upload a file in FASTA format
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Matthias Horn <>

Publication for probeCheck

probeCheck in publications

 (22)
PMCID: 5897508
PMID: 29681910
DOI: 10.3389/fpls.2018.00431

[…] gene sequence accession no. mf664204; ) was chosen as suitable non-target species, since it showed one single mismatch in the target sequence of the probe (5′-gccacccatggtattgctacc-3′) according to probecheck search (). fish was performed on paraformaldehyde-fixed cells at 10, 20, and 30% formamide onto poly-l-lysine coated glass slides, using a 50 ml screw-cap tube as humid chamber. […]

PMCID: 5861843
PMID: 29330187
DOI: 10.1128/AEM.02267-17

[…] concentrations used in this study are listed in . probes designed with arb were checked for in silico specificity against sequences in genbank using blast and against rrna sequence databases using probecheck (). the specificity was also tested experimentally against mismatched 16s rrna gene sequences of either reference strains or symbionts. general probes for bacteria (eub338 i to iii), […]

PMCID: 5661172
PMID: 29118739
DOI: 10.3389/fmicb.2017.02017

[…] genes from all species with bioedit (). the specificity of the primers was evaluated in silico against the latest sequence collections of established 16s sequence databases of bacterial genes using probecheck (), as well as experimentally using a mix of all species genomic dna isolated from pure cultures. experimentally, we did not observe cross-amplification among target species in mock […]

PMCID: 5606690
PMID: 28724850
DOI: 10.1264/jsme2.ME17028

[…] rrna (gv, vib572a and vib749) (, , ) were selected from the literature based on their specificity and closest melting temperature (tm) (). the specificity of each probe was tested in silico with the probecheck webserver (http://131.130.66.200/cgi-bin/probecheck/content.pl?id=home/) (). since we used multiple probes in the same hybridization solution, the presence of secondary structures within […]

PMCID: 5570309
PMID: 28837676
DOI: 10.1371/journal.pone.0183516

[…] on four gbm cases with strong alk immunopositivity using the vysis lsi alk break-apart rearrangement probe (abbott molecular, abbott park, il, usa), according to the manufacturer’s instructions. probecheck alk positive control slides (abbott molecular) were also used as a positive control for alk gene rearrangement., genomic dna was extracted from ffpe sections using the qiaamp dna ffpe […]


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probeCheck institution(s)
Department of Microbial Ecology, Universität Wien, Wien, Austria; Department of Genome Oriented Bioinformatics, Technische Universität München, Am Forum, Freising, Germany

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