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Table 2 illustrates the result of annotations comparison, showing that the AAMG annotation is 92.94 % similar to the one from NCBI, whereas the RAST annotation is only 83.02%% similar.
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The result of annotation was then used to identify statistically significantly enriched pathways, diseases and GO terms using protein-coding genes from the whole human genome set (20,192 genes) as background.
However, these might be also a result of annotation or sequencing errors.
Also hybrid prediction methods and the result of annotation pipelines can be incorporated into IPred.
The species specific genes were checked to ensure that they are not simply a result of annotation errors.
In Additional file 1: Section 3 we provide the comparison results of annotations by different AMs for the additional three genomes (Escherichia coli (E. coli) K-12 strain, E. coli TY2482 strain and Candidatus Carsonella ruddii DC (C. ruddii DC)).
Of these, 4152 unigenes could be annotated using all seven databases, which accounted for 6.66% of the total number of unigenes (Table 1), the detailed results of annotation is listed in Additional file 2: Table S2.
Table 1 summarizes the main results of annotation.
All the pathways described below were the results of annotation only inferred by bioinfomatics.
The results of annotation also can be accessed through the Pepper GeneChip database or [See Additional File 2: Table S2].
The results of annotation can be accessed and queried through the pepper GeneChip database [See list of URLs] or [See Additional File 2: Table S1].
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