mathFISH statistics

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mathFISH specifications

Information


Unique identifier OMICS_16675
Name mathFISH
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Daniel Noguera <>

Information


Unique identifier OMICS_16675
Name mathFISH
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Windows
Programming languages Javascript
Computer skills Advanced
Maintained Yes

Versioning


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Maintainer


  • person_outline Daniel Noguera <>

Publication for mathFISH

mathFISH in publications

 (17)
PMCID: 5604061
PMID: 28959250
DOI: 10.3389/fmicb.2017.01771

[…] newly designed by evaluating probes for the rca cluster with increased group coverage compared to probe rca826 () by using the probe design tool in arb (). analyses of hybridization efficiency via mathfish (supplementary table ; ) as well as hybridization with rca isolate rca23 (planktomarina temperata, genbank accession number gq369962, supplementary figure ) resulted in best efficiency […]

PMCID: 5562702
PMID: 28821872
DOI: 10.1038/s41598-017-09355-2

[…] using helicobacter-specific probe hel395f with alexa fluor 488 (5′-ckaaawccktcatcctccac-3′) (designed in this study). formamide concentration (set to 30%) and specificity was predicted using mathfish. after 4′-6-diamidino-2-phenylindole (dapi) staining, samples were observed under a confocal laser scanning microscope (tcs-sp8; leica microsystems, wetzlar, germany) equipped with filters […]

PMCID: 5481317
PMID: 28690595
DOI: 10.3389/fmicb.2017.01134

[…] the genome annotations are available on the ‘microscope’ website., phylogenetic analysis and probe design was performed with the arb software (). potential probes were assessed in silico with the mathfish software (). the ribosomal database project (rdp) probe match function was used to screen for non-target sequences with single base indels (; ). in order to improve the fluorescence in situ […]

PMCID: 5476839
PMID: 28676800
DOI: 10.3389/fmicb.2017.01135

[…] in the mvs, we designed a new oligonucleotide probe atri578 (table ), which can be used to detect a broad range of atribacterial sequences in the arb silva database by using arb software and mathfish (; ). the coverage of atri578 to atribacterial sequences determined by testprobe3.0 with the silva database ssu128 is 70.6% and only two sequences in the outgroup are no-mismtach to atri578. […]

PMCID: 5338771
PMID: 28264042
DOI: 10.1371/journal.pone.0172888

[…] cy5 (). formamide concentration was adjusted to 5%., oligonucleotide probes targeting the members of interests were designed using arb software []. the designed probes were first evaluated using mathfish []. if a thermodynamic value of a designed probe did not reach to the threshold (δg°overall = -13 kj/mol), the probe was elongated or locked nucleic acid (lna) was introduced []. […]


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mathFISH institution(s)
Department of Civil and Environmental Engineering, University of Wisconsin–Madison, Madison, WI, USA
mathFISH funding source(s)
This research was supported by National Science Foundation grant CBET-0606894 and the Office of Science, Department of Energy, under grant DE-FG02-07ER64495.

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