Probe/primer details
| LGC354C | Tested for in situ hybridization. |
| Accession no. | pB-197 |
| Taxonomy | Firmicutes; Bacteria |
| Specificity | Firmicutes (Gram-positive bacteria with low G+C content) |
| Category | higher taxonomic levels |
| Target rRNA | 16S rRNA |
| Position | 354-371 |
| Sequence | 5'- CCG AAG ATT CCC TAC TGC -3' |
| G+C content [%] | 56 |
| Length [nt] | 18 |
| Check specificity/coverage | 
|
| Formamide [%] | 35 |
| Hybridization efficiency |  |
| References | Specific oligonucleotide probes for in situ detection of a major group of gram-positive bacteria with low DNA G + C content. Meier H, Amann R, Ludwig W, Schleifer KH. Systematic and applied microbiology. 1999. Pubmed |
| Remarks | Use probes LGC354A, LGC354B, and LGC354C in equimolar mixture to detect most Firmicutes.ltbrgtAlso see probeBase table lta href=http://www.microbial-ecology.de/probebase/probecoverage.htmlgtCoverage of group-specific probeslt/agt. |
| Used in Microarray | SRP-PhyloChip Freshwater Sediment-Microarray |
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.
