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The order of proteins shown in both Tables 1 and 2 stood in general agreement with the relative abundance of each protein studied within any given sample, but there were exceptions to this rule.
For this purpose, we binned the proteins into 114 bins of 10 proteins, respecting the order of proteins in the clustering above, and calculated the number of interactions between every bin pair.
Solutions to this problem include the use of longer 2As (with a favourable upstream context) or modifying the order of proteins comprising polyproteins.
By swapping the order of proteins in several artificial polyproteins the stoichiometry was affected by the gene upstream of 2A [ 56, 57].
This relatively good performance means that there is a substantial amount of information about the relative duplication order of proteins encoded in the network.
The cluster file was loaded onto Treeview (version 1.60; http://rana.lbl.gov/EisenSoftware.htm) to generate a 2D branched-tree image including the phylogenic order of proteins and domain entries.
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We have found that autoantibodies consistently appear years before diagnosis of SLE within this cohort of patients [14]; however, we have not previously defined the historical order of protein-specific autoantibody appearance with the purpose being to identify the autoantibodies that first bind lupus autoantigens.
The relative order of protein-coding and rRNA genes is conserved, whereas the arrangement of tRNA genes is more variable.
Only D. gregarium differed in the order of protein-encoding genes, with nad6 changing position relative to other protein encoding and rRNA genes, as described in [ 18].
While the gene order of protein coding genes is identical among species, the position of four tRNAs (GWHC), within a cluster of seven tRNAs varies between species.
Successive synonymous codon pair represents the order of protein-coding sequences rather than their composition, which is different from single codon use.
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