Of special interest is the assignment of EST entry AU234573, representing BflGb11, to notochord tissue, as this facilitates further studies of the amphioxus globin components, which possibly serve to supply O2 to sustain the contractile function of notochord cells [ 29].
The assignments of MvirDB entries classified as 'virulence protein' show a great diversity regarding their function.
A * indicates the Superfamily database was used to predict domain assignments of PDB entries not yet classified in SCOP.
Then we used KEGG Orthology (KO) [27] to functionally cluster these ESTs into families, resulting in the assignment of 1,020 KO entries to 2,169 ESTs (Table 2).
As searches were carried out without species restriction, the correct assignment of matches to mouse entries served as an additional internal control.
This highlights another general problem with regard to assignment of function where database entries are sometimes not updated after the initial annotation.
Based on the assignment to COG entries (see File S1), a total of 4,762 reads were classified as potentially coding for enzymes involved in the degradation of complex polymers, namely cellulose, hemicellulose, and lignin (Figure 4a).
However, possible limitations in the study design in the second study are, among others, insufficient assessment of exposure time to metformin, and the assignment of an arbitrary artificial study entry date.
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