Table 1

Accuracies of taxonomic group predictions based on GC-normalized codon usage profiles

Taxonomic group

insect*

bacteria*

amoebozoa*

fungi*

nematode*

plant *


Insects

61.1 ± 0.7

6.8 ± 0.5

0.3 ± 0.1

7 ± 0.4

22.0 ± 0.3

2.8 ± 0.2

Bacteria

8.5 ± 0.2

85.5 ± 0.4

0 ± 0

1.9 ± 0.1

3.6 ± 0.2

0.5 ± 0.1

Amoebozoa

2.2 ± 0.6

1.5 ± 0.3

82.9 ± 1.2

1.7 ± 0.7

10.8 ± 1.7

0.9 ± 0.6

Fungi

10.3 ± 0.6

1.3 ± 0.1

0.2 ± 0.1

71.3 ± 0.7

9.1 ± 0.5

7.9 ± 0.3

Nematodes

12.0 ± 0.4

5.5 ± 0.2

0.5 ± 0.1

7.1 ± 0.2

71.9 ± 0.6

3.0 ± 0.2

Plants

6.8 ± 0.8

2.9 ± 0.4

0.3 ± 0.1

18.1 ± 0.6

13.9 ± 0.9

58.0 ± 1.2


Accuracy was measured using ten randomized data sets including equal number of sequences per species (see Methods). For each taxonomic group (rows), we calculated the mean percentage of predictions for all possible classifications, the "*" indicates the predicted taxonomic group (columns). For instance, while 61.1% of insect genes are correctly recognized as insect sequences based on their codon usage, 22.0% are mistaken as nematode genes.

Rödelsperger and Sommer BMC Evolutionary Biology 2011 11:239   doi:10.1186/1471-2148-11-239

Open Data