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In brief, the binary code strategy posits that stably folded proteins can be encoded by specifying the sequence pattern of polar and nonpolar residues (the binary pattern) to coincide with the exposed and buried parts of a structure, respectively.
A read r, if its sequence occurs in the transcriptome, corresponds to a path in G, and conversely there is only one path in G that spells out r. Therefore, r can be encoded by specifying a path in G by listing a sequence of nodes.
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This exposes the notion of viewing metabolism from a completely different perspective, with focus on the enzymes, regulators, and structural elements that are encoded by genes that specify the amino acid sequences, and hence encode the various interactions, be they regulatory or catalytic.
The model circuits we consider have N = 3 genes and are encoded by a genotype that specifies both the topology or "wiring" of the circuit and each gene's signal-integration logic, i.e., how the gene's regulatory region integrates signals from other genes to determine the gene's expression state.
The GP.Dantu glycophorin is specified by a hybrid gene whose N-terminal sequence is encoded by the GYPB gene and C-terminal sequence by the GYPA gene.
The Ectocarpus genome encodes two proteins that are highly similar to Erv1/Alr: the first is presumably the mitochondrial sulfhydryl oxidase (Esi0202_0015, Fig. S1F) whereas a second gene (Esi0052_0149) is encoded by an inserted viral genome similar to EsV-1 [60] and its role, if any, remains to be specified.
In mammals, the protocadherins are encoded by three closely-linked clusters (α, β and γ) of tandem genes and are hypothesized to provide a molecular code for specifying the remarkably-diverse neural connections in the central nervous system.
And yet only 20 amino acids are encoded by DNA in all life forms.
The S. aureus QS is encoded by the agr operon where agrD encodes the autoinducer.
The false memories were encoded by brain cells in the same way as real memories are sealed in.
p16 is encoded by CDKN2A.
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