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Table 3 Percentage of perfectly aligned queries.

From: Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species

  

BLAT

Exnrt.

BLAT

Exnrt.

Species

Scipio (automatic assembling)

with manual assembling

without assembling

Bombyx mori p50T

25.0

0.0

25.0

0.0

12.5

Drosophila simulans

37.8

2.7

21.6

2.7

16.2

Bombyx mori str. Dazao

15.6

3.1

12.5

0.0

9.4

Nasonia vitripennis (contigs)

71.4

11.4

57.1

11.4

54.3

Nasonia vitripennis (scaffolds)

68.6

11.4

65.7

11.4

65.7

Drosophila sechellia

63.2

7.9

55.3

2.6

55.3

Aedes aegypti

87.5

7.5

52.5

7.5

50.0

Daphnia pulex

88.1

0.0

76.2

0.0

76.2

Anopheles gambiae

94.6

8.1

73.0

8.1

73.0

Drosophila melanogaster

100.0

10.5

86.8

10.5

86.8

Aspergillus niger

86.7

6.7

73.3

6.7

73.3

Homo sapiens

62.5

0.0

50.0

0.0

50.0

Macaca mulatta

12.5

0.0

10.0

0.0

10.0

total

64.5

5.5

51.7

4.8

50.3

  1. The number of query sequences that were predicted by the programs exactly at the correct location, with 100 % matching residues, without frameshifts or false positives. This figure reveals the amount of workload needed for manual postprocessing of the hits.