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Probe/primer details

Name 804(Dsb804)
Full name
(Alm et al. 1996)
Accession no. pB-9
Taxonomy Desulfobacteraceae; Desulfobacterales; Deltaproteobacteria; delta/epsilon subdivisions; Proteobacteria; Bacteria
Specificity Some Desulfobacteraceae
Category sulfate-reducing microbes
Target rRNA 16S rRNA
Position 804-821
Sequence 5'- CAA CGT TTA CTG CGT GGA -3'
G+C content [%] 50
Length [nt] 18
Check specificity/coverage
Hybridization efficiency

Degradative capacities and 16S rRNA-targeted whole-cell hybridization of sulfate-reducing bacteria in an anaerobic enrichment culture utilizing alkylbenzenes from crude oil. Rabus R, Fukui M, Wilkes H, Widdle F. Applied and environmental microbiology. 1996. Pubmed

Devereux R., Kane M. D., Winfrey J. and Stahl D. A. (1992). Genus- and group-specific hybridization probes for determinative and environmental studies of sulfate-reducing bacteria. Syst. Appl. Microbiol. 15: 601-609

Remarks Probe was tested for FISH, but it showed no or a very weak fluorescence signal
Used in Microarray SRP-PhyloChip


Name (Alm et al., 1996). Probe designation according to Alm, E. W., Oerther, D. B., Larsen, N., Stahl, D. A., Raskin, L. (1996). The oligonucleotide probe database. Appl Environ Microbiol 62: 3557-9. Abstract (PUBMED).
Position. Probe position according to the E. coli gene numbering.
Sequence. Sequence in IUPAC code: R=G/A, Y=T/C, M=A/C, K=G/T, S=G/C, W=A/T, H=A/C/T, B=G/T/C, V=G/C/A, D=G/A/T, N=G/A/T/C
Tm. Dissoziation temperature according to: Tm=64.9 + 41 x ((G + C - 16.4)/length).
Hybridization efficiency. Use this tool to assess in silico sensitivity (i.e. the hybridization efficiency of the oligonucleotide with its fully complementary target sequence, calculated with ProbeMelt.
Formamide. Percent formamide in the hybridization buffer for optimal hybridization conditions in FISH experiments.
Coverage. Coverage of the three domains calculated using the SILVA reference database 106 if no or a single mismatch is allowed. The detailed method is described in Klindworth et al., 2012. Nucleic Acids Res. 10.1093/nar/gks808 Full Text
Check specificity/coverage. Use these options to reveal the in silico specificity (i.e. number of matching rRNA sequences outside the target taxon) and coverage (i.e. percentage of matching rRNA sequences within the target taxon) of an oligonucleotide against the most recent SSU and LSU rRNA sequence databases.