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In order to obtain insight into these questions and identify mRNA primary structural features that influence mRNA decoding error, we have developed a software package, statistical and graphical tools to study codon-pairs corresponding to ribosomal A- and P-site codons, using genome wide approaches (ANACONDA vs 1.0) [29], [29].
These peptides were grouped into two families based on their primary structural features.
The VSGs contain the same primary structural features as found in previously characterised VSGs.
Has-Som possesses a 17 residue signal sequence and shares some primary structural features with the ependymin proteins, in particular 6 cysteine residues, 4 of which are highly conserved (Fig. 11E), and two putative N-linked glycosylation sites (Fig. 11A).
Similarly, the periplasmic domains of the phiCbK-like and P2 OM spanins are remarkably parallel in primary structural features, with an N-terminal domain that is very enriched in proline residues and a C-terminal segment predicted to be alpha-helical but containing a single distal proline.
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The primary structural feature of interest is whether everybody aligns with everybody else, or whether the network tends to be composed of factions or 'coalitions' [9],[9]].
This central pseudoknot (PK) is formed by helix 2 (h2), and is the primary structural feature that leads to the positioning of the head domain upon the platform domain.
Two main structural features are noticeable.
Therefore explanations invoking GC content effects in particular, and base-composition effects in general, cannot account for important primary-structural features of mammalian and avian coding regions.
The slopes, moreover, range between 1.0 and 2.0 indicating that the primary-structural features due to 64×4 NBDM are of the same order of magnitude as those observed in native intron DNA.
Analysis of primary and secondary structural features of the BM2 signal has revealed that it contains a short TURBS (of 45 nt) which is largely single-stranded, with motif 1 likely to be located in the apical loop of a metastable stem-loop structure when the ribosome is positioned at the termination codon of the upstream ORF [11].
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