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Table 2 Test scenario 1: Reconstruction of the Loxodonta africana dynein heavy chain genes in the whole genome sequence based on human protein sequences

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

Tool

Predicted genes

Missing exons1

Wrong exons2

Exon sens. %

Exon sens. (ov.)3 %

Exon spec. %

Nucl. sens. %

Nucl. spec. %

Execution time per prot. seq.

Scipio 1.54

16

11

6

93.4

99.1

93.3

98.7

99.8

70 m 46s

Exonerate5

2145

6

5669

94.8

99.5

16.5

99.7

18.5

123 m 23s

Exonerate6

16

287

62

73.4

76.1

90.2

76.1

94.3

121 m 27s

Augustus7

1374928

0

3909434

47.9

100.0

0.0

100.0

0.3

> 10 days

BLAT8

-

9

264228

19.6

99.3

0.1

97.4

2.6

7 m 24s

Scipio 1.04

16

14

46

86.1

98.8

83.2

97.9

99.4

8 m 24s

  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 Parameters: --model protein2genome
  6. 6 Parameters: --model protein2genome --bestn 1
  7. 7 Parameters: --species = human --genemodel = exactlyone (for more parameters see Additional file 5)
  8. 8 Parameters as in 4: -tileSize = 7 -minIdentity = 54 -minScore = 15 -oneOff = 1