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 in publications

 (33)
PMCID: 5131408
PMID: 27905892
DOI: 10.1186/s12883-016-0769-y

[…] (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/)., we obtained hek293t and glioma cell lines u251, u87, shg44 from cell bank of chinese academy of sciences, shanghai, china. dmem with 10% fetal bovine serum (gibco, carlsbad, ca, usa) […]

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

[…] 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 […]

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

[…] (additional file )., 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 […]

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

[…] 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 […]

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

[…] and 10.5 µl water free from rnase. denaturation was performed at 42°c for 60 min and annealing at 95°c for 5 min., 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, […]


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