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Table 3 Test scenario 2: Reconstruction of the Loxodonta africana dynein heavy chain gene structures in the respective gene regions based on human protein sequences

From: Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio

Tool

Pred. genes

Missing exons1

Wrong exons2

Exon sens. %

Exon sens. (ov.)3 %

Exon spec. %

Nucl. sens. %

Nucl. spec. %

Scipio 1.54

16

13

6

93.1

98.9

93.1

98.6

99.8

Scipio 1.55

16

4

7

94.7

99.7

93.7

99.2

99.8

Prosplign6

16

1

41

95.7

99.9

92.6

99.9

98.7

Exonerate7

32

7

6

94.8

99.4

94.6

99.6

99.5

Exonerate8

16

255

4

75.7

78.8

95.6

79.2

99.7

Prot_map9

16

4

27

91.7

99.7

86.2

99.3

99.7

Fgenesh+10

16

10

10

94.9

99.2

94.8

99.0

99.7

Wise211

39

3

16

93.3

99.8

91.2

99.7

98.9

Augustus12

16

132

111

81.9

89.0

83.2

89.9

88.7

Fgenesh10

161

111

342

80.2

90.8

67.3

91.8

62.3

Genscan13

194

138

520

76.3

88.5

57.9

90.4

55.3

BLAT14

-

16

19

19.9

98.7

19.4

97.0

98.9

Scipio 1.04

16

16

10

86.2

98.7

85.9

97.8

99.8

  1. 1 Number of annotated exons, which are not overlapped by any predicted exon
  2. 2 Number of predicted exons, which are not overlapped by any annotated exon
  3. 3 Number annotated exons, which are overlapped by at least one predicted exon divided by the number of annotated exons
  4. 4 Mammalia cross species default options (for detailed parameters see Additional file 5)
  5. 5 Mammalia cross species default options; -tileSize = 6 (for detailed parameters see Additional file 5)
  6. 6 Parameters: -full -two_stages
  7. 7 Parameters: --model protein2genome
  8. 8 Parameters: --model protein2genome --bestn 1
  9. 9 Similarity: Weak; Search for one best alignment only (for more parameters see Additional file 5)
  10. 10 Organism: Human
  11. 11 Parameters: -both
  12. 12 Parameters: --species = human --genemodel = exactlyone (for more parameters see Additional file 5)
  13. 13 Organism: Vertebrate; Suboptimal exon cutoff: 1.00
  14. 14 Parameters as in 4: -tileSize = 7 -minIdentity = 54 -minScore = 15 -oneOff = 1