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Table 3 Alignment of DNA for 812 bidirectionally sequenced Hort1A cDNA sequences (A) and 550 Hort16A predicted protein sequences (B & C) with the Red5, original ‘Hongyang’ [14], and revised ‘Hongyang’ [18] gene model sets

From: A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

 

Red5 Models

Original Hongyang Models

Revised Hongyang Models

A

Hort16A cDNA with BLAT match identitya > = 60%

635

465

510

Hort16A cDNA with BLAT match identitya <  60%

165

289

263

Hort16A cDNA with no match

12

58

39

 

812

812

812

B

Hort16A predicted protein with BLAT match identitya > = 60%

541

462

481

Hort16A predicted protein with BLAT match identitya <  60%

6

76

60

Hort16A predicted protein with no match

3

12

9

 

550

550

550

C

% Identity Rangea

 0–59

6

76

60

 60–64

2

23

7

 65–69

2

21

15

 70–74

5

20

16

 75–79

2

36

19

 80–84

13

39

28

 85–89

17

54

47

 90–94

17

72

67

 95–99

339

168

231

 100

144

29

51

  1. a% identity was calculated as the number of matched bases (A) or matched amino acids (B & C) between Hort16A and the named gene set divided by the total length of the Hort16A cds sequence (A) or predicted protein sequence (B & C)
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BMC Genomics

ISSN: 1471-2164

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