probeCheck statistics

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Citations per year

Number of citations per year for the bioinformatics software tool probeCheck
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Tool usage distribution map

This map represents all the scientific publications referring to probeCheck per scientific context
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Protocols

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 citations

 (30)
library_books

Specific Fluorescence in Situ Hybridization (FISH) Test to Highlight Colonization of Xylem Vessels by Xylella fastidiosa in Naturally Infected Olive Trees (Olea europaea L.)

2018
Front Plant Sci
PMCID: 5897508
PMID: 29681910
DOI: 10.3389/fpls.2018.00431

[…] A 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. Same than f […]

library_books

Acquisition of a Novel Sulfur Oxidizing Symbiont in the Gutless Marine Worm Inanidrilus exumae

2018
Appl Environ Microbiol
PMCID: 5861843
PMID: 29330187
DOI: 10.1128/AEM.02267-17

[…] de 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), Gammap […]

library_books

Guideline from Japanese Society of Echocardiography: 2018 focused update incorporated into Guidance for the Management and Maintenance of Echocardiography Equipment

2018
PMCID: 5818545
PMID: 29362979
DOI: 10.1007/s12574-018-0370-z

[…] r cable, or ECG monitor cable. Check the connections.Check that the LAN cable (for input/output of electronic patient records) is properly connected to the LAN outlet. Check for damage.Inspecting the probeCheck for any abnormalities such as damage or cracks to the acoustic lens surface or the handle.Check for any cracks, damage, or broken pins in the connector (connection with the main device).Che […]

library_books

Resolving Species Level Changes in a Representative Soil Bacterial Community Using Microfluidic Quantitative PCR

2017
Front Microbiol
PMCID: 5661172
PMID: 29118739
DOI: 10.3389/fmicb.2017.02017

[…] A 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 communi […]

library_books

Spatiotemporal Dynamics of Total Viable Vibrio spp. in a NW Mediterranean Coastal Area

2017
PMCID: 5606690
PMID: 28724850
DOI: 10.1264/jsme2.ME17028

[…] The specificity of probes was first analyzed in silico using the ProbeCheck webserver and databases from RDPII, SILVA, and Greengenes. A total of 3,509 sequences belonging to members of Vibrionaceae and including sequences from 103 different species of the genera V […]

library_books

Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters

2017
Microbiome
PMCID: 5610417
PMID: 28938908
DOI: 10.1186/s40168-017-0344-9

[…] nd a corresponding competitor probe c1MEVE845 (5′- TTA GCT GCG TTA CTC AAT GAG-3′) were newly designed based on the non-redundant ARB-SILVA database version 111Ref [] using the probe tools of ARB [], probeCheck [], and RDP II []. Dissociation-curve analysis [] with the perfectly matched type strain Methyloversatilis universalis showed that probe MEVE845 should be applied at 25% formamide to ensure […]


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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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