Probe/primer details
| LPLANG | Tested for in situ hybridization. |
| Accession no. | pB-3914 |
| Taxonomy | Lactobacillus plantarum; Lactobacillus; Lactobacillaceae; Lactobacillales; Bacilli; Firmicutes; Bacteria |
| Specificity | Lactobacillus plantarum 423 |
| Category | animal and human associated microbiota intestinal microbiota |
| Target rRNA | 16S rRNA |
| Sequence | 5'- TAT CAT TGC CAT GGT GA -3' |
| G+C content [%] | 41 |
| Check specificity/coverage | 
|
| Formamide [%] | 25 |
| Hybridization efficiency |  |
| References | Adhesion of Lactobacillus plantarum 423 and Lactobacillus salivarius 241 to the intestinal tract of piglets, as recorded with fluorescent in situ hybridization (FISH), and production of plantaricin 423 by cells colonized to the ileum. Maré L, Wolfaardt GM, Dicks LM. Journal of applied microbiology. 2006. Pubmed Mare´, L. (2005) Probiotic properties of lactic acid bacteria evaluated in a gastro-intestinal model and in in vivo pig trials. PhD dissertation, Stellenbosch University, Stellenbosch,South Africa. |
Glossary
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.
