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Table 2 RefMax vs. MAS 5.0: A Validation Study

From: Investigating the global genomic diversity of Escherichia coli using a multi-genome DNA microarray platform with novel gene prediction strategies

   

Present

Absent

Genome

Homology Bin

Genes Present

MAS5

RefMax

MAS5

RefMax

NC_000913.2

100%

5654

5651/5651

5653/5654

3/3

1/0

NC_000913.2

>98%

391

385/385

382/382

6/6

9/9

NC_000913.2

>96%

410

263/268

225/226

147/142

185/184

NC_000913.2

>94%

347

92/102

49/48

255/245

298/299

NC_000913.2

>92%

202

36/35

13/13

166/167

189/189

NC_000913.2

>90%

143

32/36

8/9

111/107

135/134

NC_000913.2

<90%

12

3/3

1/1

9/9

11/11

NC_002655.2

100%

3569

3565/3564

3558/3566

4/5

11/3

NC_002655.2

>98%

2656

2653/2653

2644/2648

3/3

12/8

NC_002655.2

>96%

1178

1053/1054

963/963

125/124

215/215

NC_002655.2

>94%

502

302/287

159/162

200/215

343/340

NC_002655.2

>92%

288

143/138

59/60

145/150

229/228

NC_002655.2

>90%

231

132/132

70/69

99/99

161/162

NC_002655.2

<90%

20

8/9

6/6

12/11

14/14

NC_002695.1

100%

3473

3471/3472

3466/3464

2/1

7/9

NC_002695.1

>98%

2655

2652/2652

2646/2641

3/3

9/14

NC_002695.1

>96%

1164

1036/1031

945/936

128/133

219/228

NC_002695.1

>94%

511

302/291

169/167

209/220

342/344

NC_002695.1

>92%

291

140/138

66/66

151/153

225/225

NC_002695.1

>90%

208

108/102

52/52

100/106

156/156

NC_002695.1

<90%

18

7/6

5/5

11/12

13/13

NC_004431.1

100%

3112

3111/-

3111/-

1/-

1/-

NC_004431.1

>98%

1816

1816/-

1814/-

-/-

2/-

NC_004431.1

>96%

1585

1494/-

1450/-

91/-

135/-

NC_004431.1

>94%

509

304/-

247/-

205/-

262/-

NC_004431.1

>92%

261

96/-

55/-

165/-

206/-

NC_004431.1

>90%

198

90/-

48/-

108/-

150/-

NC_004431.1

<90%

16

7/-

6/-

9/-

10/-

  1. Gene present/absent calls were determined for the 4 sequenced reference strains represented on the array using either the RefMax or MAS 5.0 gene detection methods. Genome corresponds to the accession number of the genome/strain being interrogated. Homology Bin corresponds to the percentage by which a probe set consensus sequence matches the target genome sequence. Genes Present corresponds to the number of genes present on the array which fall into a particular Homology Bin (this is also the maximum number of correct "present" calls). Present or Absent calls were determined from either the MAS 5.0 or RefMax method and are shown under the "MAS5" and "RefMax" headings. Strains MG1655, EDL933, and Sakai were each performed in duplicate to show the reproducibility of each method. Independent measurements are indicated by a "/" under the Present and Absent headers.
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BMC Genomics

ISSN: 1471-2164

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