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. 2013 Sep 25;14:654. doi: 10.1186/1471-2164-14-654

Table 7.

Estimating annotation quality using protein features and sequence data

Organism Domain score outlier +,-,truncated domain Length outlier Conserved downstream Methionine No protein in main cluster Negative sum-of-logs score Core proteins
*human
0.000
0.021
0.017
0.028
0.012
10.256
7419
*housemouse
0.002
0.033
0.036
0.051
0.049
8.135
6811
*dog
0.005
0.068
0.115
0.051
0.030
7.268
6495
*African savanna elephant
0.006
0.096
0.163
0.038
0.042
6.816
5685
*domestic guinea pig
0.005
0.093
0.158
0.047
0.045
6.812
5699
*cow
0.008
0.082
0.101
0.041
0.060
6.795
6394
pygmy chimpanzee
0.003
0.100
0.146
0.081
0.044
6.764
6584
*horse
0.006
0.105
0.149
0.054
0.042
6.699
5838
rabbit
0.004
0.122
0.189
0.050
0.052
6.646
4159
chimpanzee
0.005
0.108
0.138
0.068
0.048
6.600
6455
*norway rat
0.008
0.077
0.084
0.061
0.080
6.600
5851
giant panda
0.005
0.139
0.224
0.063
0.035
6.501
5765
olive baboon
0.006
0.115
0.156
0.077
0.048
6.416
5872
*bolivian squirrel monkey
0.007
0.108
0.152
0.086
0.053
6.284
6035
white-tufted-ear marmoset
0.005
0.126
0.207
0.083
0.055
6.197
5777
domestic cat
0.005
0.193
0.254
0.070
0.041
6.178
6007
northern white-cheeked gibbon
0.006
0.148
0.195
0.077
0.056
6.151
5730
western gorilla
0.007
0.167
0.197
0.078
0.057
5.958
5722
small-eared galago
0.012
0.138
0.197
0.076
0.046
5.955
6128
gray short-tailed opossum
0.006
0.214
0.370
0.058
0.041
5.924
4500
chinese hamster
0.006
0.190
0.265
0.066
0.061
5.892
4901
sheep
0.007
0.232
0.292
0.070
0.041
5.871
5339
*chicken
0.013
0.175
0.228
0.072
0.051
5.729
3354
rhesus macaque
0.011
0.169
0.216
0.083
0.072
5.639
5466
pig
0.025
0.192
0.230
0.061
0.042
5.551
4616
sumatran orangutan
0.014
0.169
0.222
0.081
0.071
5.509
5050
*green anole
0.018
0.215
0.296
0.068
0.048
5.431
2797
nile tilapia
0.011
0.392
0.583
0.071
0.061
4.961
1296
tasmanian devil
0.016
0.337
0.478
0.082
0.054
4.933
3457
*zebrafish
0.025
0.344
0.464
0.062
0.068
4.773
1210
torafugu
0.017
0.448
0.601
0.060
0.063
4.765
1130
turkey
0.023
0.425
0.520
0.077
0.055
4.659
1821
western clawed frog
0.023
0.394
0.484
0.073
0.070
4.644
2268
platypus
0.031
0.435
0.586
0.068
0.067
4.451
1439
Average
0.010
0.187
0.256
0.066
0.052
6.111
4796
Standard deviation
0.008
0.120
0.160
0.014
0.014
1.114
1826
Correlation Contig N50
−0.290
−0.337
−0.362
−0.489
−0.434
0.719
0.319
Correlation EST count −0.164 −0.299 −0.342 −0.555 −0.395 0.684 0.263

Columns 2–7 provide fraction of genes from each species in the orthology dataset and lacking conserved protein; outlier domain score; missing, extra, or truncated domain; outlier length; conserved downstream or upstream Met; and proteins not found in largest cluster. Column 8 provides the negative sum of logs score. The last column provides the number of genes in each species that are members of a “core” set defined as ortholog sets with members from at least 17 species that each have conserved splicing to at least 3 proteins from reference species (reference species are marked with *.)