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1. Site-directed mutagenesis for FMP003: The codon harmonization algorithm was applied to the gene fragment encoding MSP142 from the FVO strain of P. falciparum (GenBank accession no. L20092).
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The basic concepts underlying the "codon harmonization" algorithm are derived from evidence provided in Thanaraj, et al, where codon usage frequency patterns from E. coli proteins having known structures were analyzed [22].
The post harmonization algorithms are described in detail in harmonization guidelines attached to this paper.
Across the cohorts, different measurement instruments were used and post harmonization algorithms were needed to merge the datasets and enable statistical analyses that allow testing cross-country differences.
Post harmonization algorithms are developed by finding a "common denominator" to merge the datasets and weights are calculated to adjust for differences in age and sex distribution across the datasets.
The algorithm was further tested by preparing a "fully harmonized" MSP142 (FVO) gene fragment (designated FMP010), which was completely recoded according to the harmonization approach described in "Materials and Methods".
The algorithm was 79.3% accurate.
"This algorithm is beautiful".
The algorithm is simple.
Baseline algorithm is the standard compression algorithm.
2. Full codon harmonization of MSP142 FVO gene: The synthetic gene sequence for the MSP142 FVO synthetic gene fragment or FMP010 (GenBank Accession no. DQ926900) was developed by applying the codon harmonization algorithm over the entire gene sequence.
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