Comparison of RefSeq protein-coding regions in human and vertebrate genomes

Fong, Jessica H; Murphy, Terence D; Pruitt, Kim D

doi:10.1186/1471-2164-14-654

BMC Genomics

Table 7 Estimating annotation quality using protein features and sequence data

From: Comparison of RefSeq protein-coding regions in human and vertebrate genomes

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 *.)

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ISSN: 1471-2164

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