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Table 1 Summary of cDNA libraries and EST data

From: Comparative analysis of differentially expressed genes in normal and white spot syndrome virus infected Penaeus monodon

 

Library

 

PmTwN

 

PmTwI

Category

Number of sequences

Total sequenced cDNA1

3':6964, 5':1036

 

3':7686, 5':1119

High quality ESTs1

3':6658, 5': 978

 

3':7276, 5':1069

cDNA clones that produced high quality ESTs

6671

 

7298

Mean EST length (bp)

678

 

652

Unique sequences

 

9622

 

Mean unique sequence length (bp)

 

678

 

Contigs

 

1364

 

Matched unique sequence (nr db)

 

2027 (21.07%2)

 

Matched unique sequence (UniProt db)

 

2026 (21.06%2)

 

Matched ESTs3 (nr db)

3022 (45.30%4)

 

3338 (45.74%4)

Matched ESTs3 (UniProt db)

2870 (43.02%4)

 

3202 (43.88%4)

  1. 1: The numbers of 3' and 5' end sequences are shown.
  2. 2: The percentage is calculated by dividing the number of unique sequences (9622) by the number of matched unique sequences (2027 and 2026, respectively).
  3. 3: Some cDNA clones have both 5' and 3' ESTs, and when both or either ESTs had matches in databases, the corresponding 5' and 3' ESTs from the same clone will be marked and only one was counted.
  4. 4: The percentage is calculated by dividing the number of cDNA clones that produced high quality ESTs (6671 or 7298) by the number of matched ESTs (3022 and 3338, respectively, or 2870 and 3202).
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BMC Genomics

ISSN: 1471-2164

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