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Table 1 Comparison of the percent unique sequences as determined by either CAP3 or Phrap analysis for the 5' and 3' ESTs represented in each of the four successive reracked clone subsets that constitute the low redundancy soybean 'unigene' set

From: Microarrays for global expression constructed with a low redundancy set of 27,500 sequenced cDNAs representing an array of developmental stages and physiological conditions of the soybean plant

Rerack order & name

Number cDNAs

No. ESTs clustereda

Cap3b

Phrapb

% Unique ESTsc Cap3 or Phrap

1. Gm-r1021

4,089

2,797, 5'

2,202 s 259 c

2,054 s 334 c

88.0% : 80.4%

1. Gm-r1021

4,089

2,797, 3'

1,836 s 413 c

1,682 s 505 c

85.4% : 78.2%

2. Gm-r1070

9,216

6,938 5'

5,566 s 620 c

5,116 s 831 c

89.2% : 78.0%

2. Gm-r1070

9,216

6,938 3'

4,284 s 1,124 c

3,900 s 1,340 c

85.7% : 75.5%

3. Gm-r1083

4,992

3,879 5'

3,426 s 200 c

3,289 s 260 c

93.5% : 79.7%

3. Gm-r1083

4,992

3,879 3'

2,474 s 599 c

2,256 s 723 c

91.5% : 76.8%

4. Gm-r1088

9,216

7,434 5'

6,295 s 521 c

5,909 s 745 c

91.7% : 89.5%

4. Gm-r1088

9,216

7,434 3'

4,719 s 1,173 c

4,152 s 1,513 c

79.3% : 76.2%

Entire set, 1–4

27,513

27,513 5d

21,873 s 2,402 c

18,663 s 3,966 c

88.2% : 81.2%

Entire set, 1–4

27,513

21,048 3'

11,959 s 4,156 c

8,341 s 5,641 c

73.0% : 63.3%

  1. a Unless otherwise noted, the ESTs included in the cluster analysis represent only the cDNAs for which both the 5' and 3' sequences are known and for which the read length is over 200 bases.
  2. b The number of singletons (s) and number of contigs (c) are shown.
  3. c The % unique sequences is the number of singletons plus the number of contigs divided by the total number of ESTs.
  4. d In this analysis, all 5' sequences were included even if the corresponding 3' sequence was not known.
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BMC Genomics

ISSN: 1471-2164

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