While ion transport and chromatin assembly genes, which are indirectly related to the lifestyle of these parasites, have constrained coding regions, they also have highly constrained upstream regions implying that their action in Plasmodium species requires tight regulatory control.
DICOM like the HL7 Clinical Document Architecture (CDA)—uses templates and constrained, coded vocabulary (SNOMED, LOINC, etc).
Even after constraining the coding region sequences to these motifs, appending overhangs for directional ligations may result in oligonucleotides that are thermodynamically prone to formation of undesired heteroduplexes or intramolecular secondary structures (hairpins, Figure 2 D).
We compare the performance of Fisher vector encoding with sparse coding and locality constrained linear coding (LLC).
From the experiments and results, we observed that Fisher vector encoding is the most computationally efficient algorithm when compared to feature mapping using sparse coding and locality constrained linear coding (LLC).
Open reading frames (ORFs), in contrast, are thought to be constrained by coding function, precluding a major role in gene regulation.
The third codon position was selected for analysis because this position is the least constrained by coding requirements.
Many of these repeats occur in genes, where they may constrain protein coding and thus gene function.
The results of these analyses (Table 2) showed in most cases Ka/Ks values not significantly different from 1.0, as expected in the differentiation of pseudogene sequences not constrained by coding of functional amino acids.
Therefore, it appears reasonable to consider additionally constrained random codes that retain the degeneracy pattern of codons inherent to the standard code (i.e., each amino acid is allotted the same number of codons as in the standard code).
