GeneFisher2 statistics

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Citations per year

Number of citations per year for the bioinformatics software tool GeneFisher2
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Tool usage distribution map

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Associated diseases

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Popular tool citations

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Protocols

GeneFisher2 specifications

Information


Unique identifier OMICS_02341
Name GeneFisher2
Alternative name GeneFisher
Interface Web user interface
Restrictions to use None
Input data Codon Usage Table, AA alignement, DNA Alignement, the consensus sequence
Input format CGC
Output data The consensus sequence of the given alignment, Noise Threshold, Conservation Threshold, Cutoff Threshold, Maximal Difference of Melting Temperature, Primer Degeneracy, Display only Unique Primer, Salt Concentration, Minimal Melting Temperature, Minimal 3' GC-Content, Maximal GC-Content, Minimal Primer Length, Oligonucleotide Concentration, Minimal GC-Content, Maximal Product Size, Maximal Primer Length, Maximal Melting Temperature, Primer 3' Length, Minimal Product Size, 3' degeneracy and Nucleotide at 3'-End.
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • BatCons2

Maintainers


  • person_outline Robert Giegerich
  • person_outline Folker Meyer
  • person_outline Chris Schleiermacher

Additional information


https://bibiserv.cebitec.uni-bielefeld.de/genefisher2?id=genefisher_manual_manual

Publication for GeneFisher2

GeneFisher2 citations

 (41)
library_books

Biochemical Defense Response: Characterizing the Plasticity of Source and Sink in Spring Wheat under Terminal Heat Stress

2017
Front Plant Sci
PMCID: 5611565
PMID: 28979274
DOI: 10.3389/fpls.2017.01603

[…] tegrity was verified on 1.2% agarose gel. First strand cDNA synthesis and qRT-PCR were done as mentioned in Kumar et al. (). Primers used for the qRT-PCR were designed from the deduced sequence using GeneFisher2 Prime designing software (http://bibiserv.techfak.uni-bielefeld.de/genefisher2/) (Table ). The Sybr chemistry (Kappa Sybr Fast Universal kit) was used for the quantification using the CFX9 […]

call_split

miR 491 regulates glioma cells proliferation by targeting TRIM28 in vitro

2016
PMCID: 5131408
PMID: 27905892
DOI: 10.1186/s12883-016-0769-y
call_split See protocol

[…] 5.1 (www.targetscan.org) and human microRNA (http://www.microrna.org/). We speculated the minimum free energy for hybridization and examined through BibiServ (http://bibiserv.techfak.uni-bielefeld.de/genefisher2/). […]

library_books

Modulation of the Immune Response by Nematode Secreted Acetylcholinesterase Revealed by Heterologous Expression in Trypanosoma musculi

2016
PLoS Pathog
PMCID: 5089771
PMID: 27802350
DOI: 10.1371/journal.ppat.1005998

[…] icidin resistance genes isolated from pMCGFPtubBlast []. Consensus sequences for α tubulin, β tubulin and paraflagellar rod (PFR) genes from other trypanosome species were generated using the program GeneFisher2 (Bielefeld University) and sequences from NCBI nucleotide and TriTryp databases. Degenerate primers for consensus sequences were used to amplify the α-β tubulin IR, the β-α tubulin IR and […]

library_books

Transcriptomic and metabolomic profiling of ionic liquid stimuli unveils enhanced secondary metabolism in Aspergillus nidulans

2016
BMC Genomics
PMCID: 4830055
PMID: 27072538
DOI: 10.1186/s12864-016-2577-6

[…] All quantitative real-time PCR (qRT-PCR) oligonucleotide pairs – based on A. nidulans gene sequences (Aspergillus Genome Database, www.aspgd.org) - were designed using the GeneFisher2 web tool (http://bibiserv.techfak.uni-bielefeld.de/genefisher2) and produced by Thermo Fisher Scientific (Additional file ). qRT-PCR analyses were performed in a CFX96 Thermal Cycler (Bio- […]

library_books

Relevance of miR 21 in regulation of tumor suppressor gene PTEN in human cervical cancer cells

2016
BMC Cancer
PMCID: 4791868
PMID: 26975392
DOI: 10.1186/s12885-016-2231-3

[…] CBI: NM_000314] was measured by semiquantitative end-point RT-PCR using the sense 5′-GGG-AAG-ACA-AGT-TCA-TGT-AC-3′ and antisense 5′-AGT-ATC-GGT-TGG-CTT-TGT-C-3′ primers which were generated using the GeneFisher2-interactive PCR primer design software []. The PCR reaction amplification conditions were 95 °C for 10 min, 95 °C for 1 min, 55 °C for 30 s and 72 °C for 1 min for 35 cycles followed by 72 […]

library_books

Correlation between the expression of hTERT gene and the clinicopathological characteristics of hepatocellular carcinoma

2015
PMCID: 4727113
PMID: 26870177
DOI: 10.3892/ol.2015.3892

[…] The primers for hTERT and internal standard GAPDH were designed as follows using Genefisher software (Bielefeld University, Bielefeld, Germany): hTERT forward, 5′-TTTCTGGAGCTGCTTGGGAA-3′ and reverse, 5′-GAAGAGCCTGAGCAGCTCGA-3′ (44-bp product); and GAPDH forward, 5′-TCCTCTGACTTCAAC […]


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