The ISME Journal - Table 3 for article: Improved group-specific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities

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Improved group-specific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities

Martin Mühling, John Woolven-Allen, J Colin Murrell and Ian Joint

Table 3. Comparison of 16S rRNA gene group-specific primers developed in this study with those used in previous studies by Blackwood et al. (2005) and Nübel et al. (1997)

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Primer pairs	Escherichia coli position	Percentage of matches within the target group	Matches outside target group
Alf684r	684–702	88.5	242
ADF681F	682–698	87.3	47
Beta682r	682–701	86.4	6
Beta680F	680–694	85.7	5
Plancto920r	920–937	47.5	6
Plancto930R	931–947	43.1	3
Firm350f	350–369	24.9	7
BLS342F	352–369	21.1	0
CFB968r	968–985	90.5	16
Cyt1020R	978–995	8.5	0
CYA361f	361–378	91.0	16
CYA359F	359–378	83.4	73
CYA785r	785–805	88.2	42
CYA781R ^a	781–805	87.2	40

The in silico analysis was carried out using the PRIMROSE program (Ashelford et al., 2002). The primers used by Blackwood et al. (2005) and Nübel et al. (1997) are indicated in bold.

^a Comparison is based on the mixture of primers CYA781R(a) and CYA781R(b) (Nübel et al., 1997).

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TABLE 3

Improved group-specific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities

Table 3. Comparison of 16S rRNA gene group-specific primers developed in this study with those used in previous studies by Blackwood et al. (2005) and Nübel et al. (1997)