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Table 3 T-RF diversity for single phylogenetic descriptions

From: PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data

Phylogenetic affiliation

dTRF (bp)

dTRF shifteda(bp)

Countsb(−)

Relative contribution to T-RFc(%)

Reference OTUd

Reference GenBank accession numbere

SW mapping scoref(−)

Normalized SW mapping scoreg(−)

Flocculent and aerobic granular sludge samples from wastewater treatment systems

Rhodocyclus tenuis

39

34

37

4.8

3160

AB200295

363

0.917

 

199

194

1

25.0

3160

AB200295

248

0.648

 

205

200

3

100.0

3160

AF204247

314

0.858

 

210

205

1

100.0

3160

AF204247

211

0.699

 

218

213

11

91.7

3160

AB200295

356

0.942

 

219

214

769

99.6

3160

AB200295

371

0.949

 

220

215

6

37.5

3160

AF502230

318

0.817

 

221

216

1

7.7

3160

AF502230

276

0.865

 

225

220

2

3.7

3160

AB200295

206

0.703

 

252

247

3

100.0

3160

AB200295

305

0.762

 

253

248

9

100.0

3160

AB200295

228

0.752

 

257

252

1

20.0

3160

AF502230

241

0.660

Groundwater samples from aquifers contaminated with chloroethenes

Dehalococcoides spp.

166

161

1

100.0

1368

EF059529

290

0.775

 

168

163

143

100.0

1368

EF059529

241

0.717

 

169

164

2

100.0

1368

EF059529

331

0.768

 

170

165

2

100.0

1368

EF059529

241

0.693

 

171

166

1

50.0

1368

EF059529

303

0.783

 

173

168

1

100.0

1368

EF059529

241

0.717

 

176

171

1

100.0

1369

DQ833317

211

0.687

 

179

174

1

100.0

1369

DQ833317

193

0.629

 

188

183

4

66.7

1369

DQ833340

464

0.947

  1. a Digital T-RF obtained after having shifted the digital dataset with the most probable average cross-correlation lag.
  2. b Number of reads of the target phylotype that contribute to the T-RF.
  3. c Diverse bacterial affiliates can contribute to the same T-RF.
  4. d Reference OTU from the Greengenes public database obtained after mapping.
  5. e GenBank accession numbers provided by Greengenes for reference sequences.
  6. f Best SW mapping score obtained.
  7. g SW mapping score normalized by the read length.