Table 5

CDS assessment at the transcript and gene levels

Transcript

Gene



TSn

TSp

GSn

GSp

Ratio CDS/UTR


Category 1

AUGUSTUS-any

22.65%

35.59%

47.97%

35.59%

100.00%

FGENESH++

36.21%

41.61%

69.93%

42.09%

78.25%

JIGSAW

34.05%

65.95%

72.64%

65.95%

100.00%

PAIRAGON-any

39.29%

60.34%

69.59%

61.32%

62.92%

Category 2

AUGUSTUS-abinit

11.09%

17.22%

24.32%

17.22%

100.00%

GENEMARK.hmm-A

6.93%

3.24%

15.20%

3.24%

100.00%

GENEMARK.hmm-B

7.70%

7.91%

16.89%

7.91%

100.00%

GENEZILLA

9.09%

8.84%

19.59%

8.84%

100.00%

Category 3

ACEVIEW

44.68%

19.31%

63.51%

48.65%

49.15%

AUGUSTUS-EST

22.50%

37.01%

47.64%

37.01%

100.00%

ENSEMBL

39.75%

54.64%

71.62%

67.32%

65.77%

EXOGEAN

42.53%

52.44%

63.18%

80.82%

59.60%

EXONHUNTER

10.48%

6.33%

21.96%

6.33%

100.00%

PAIRAGON+NSCAN_EST

39.29%

60.64%

69.59%

61.71%

62.89%

Category 4

AUGUSTUS-dual

12.33%

18.64%

26.01%

18.64%

100.00%

DOGFISH

5.08%

14.61%

10.81%

14.61%

100.00%

MARS

15.87%

15.11%

33.45%

24.94%

100.00%

NSCAN

16.95%

36.71%

35.47%

36.71%

79.80%

SAGA

2.16%

3.44%

4.39%

3.44%

100.00%

UCSC Tracks

ACEMBLY

33.90%

7.96%

54.39%

21.24%

48.56%

CCDSgene

28.97%

85.58%

55.41%

89.39%

100.00%

ECgene

56.86%

8.84%

79.05%

12.42%

46.11%

ENSgene

40.52%

54.09%

73.99%

68.30%

65.62%

GENEID

4.78%

8.78%

10.47%

8.78%

100.00%

GENSCAN

7.40%

10.13%

15.54%

10.13%

100.00%

KNOWNgene

43.45%

46.93%

77.03%

72.79%

60.03%

MGCgene

23.73%

78.24%

49.32%

82.56%

63.43%

REFgene

41.91%

75.21%

77.03%

82.76%

61.82%

SGPgene

8.17%

12.59%

17.57%

12.59%

100.00%

TWINSCAN

10.63%

20.25%

22.30%

20.25%

100.00%


The ratio CDS/UTR was obtained by summing up all the coding exons' lengths and dividing by the sum of all the exons' lengths. The ratio CDS/UTR for the annotations is 36.78%.

Guig√≥ et al. Genome Biology 2006 7(Suppl 1):S2   doi:10.1186/gb-2006-7-s1-s2