public async Task <string> OptimizeProteinSequence(string proteinSequence, string organismId)
{
if (string.IsNullOrWhiteSpace(proteinSequence) || string.IsNullOrWhiteSpace(organismId))
{
throw new ArgumentNullException();
}
string optimizedDNASequence = "";
var allAminoAcids = await unitOfWork.GetAll <AminoAcid>().Include(x => x.Codons).ToListAsync();
var organism = unitOfWork.GetById <Organism>(organismId);
foreach (Char aminoCode in proteinSequence)
{
string aminoAcidCode = aminoCode.ToString();
AminoAcid aminoAcid = allAminoAcids.Single(x => x.Code == aminoAcidCode);
List <CodonUsage> codonUsages = new List <CodonUsage>();
foreach (Codon codon in aminoAcid.Codons)
{
CodonUsage codonUsage = organism.CodonUsages.SingleOrDefault(x => x.Codon.Triplet == codon.Triplet);
if (codonUsage != null)
{
codonUsages.Add(codonUsage);
}
}
var maxFrequency = codonUsages.Max(x => x.Frequency);
CodonUsage maxCodonUsage = codonUsages.First(x => x.Frequency == maxFrequency);
optimizedDNASequence += maxCodonUsage.Codon.Triplet;
}
return(optimizedDNASequence);
}
public CodonUsage CreateCodonUsage()
{
var codonUsage = new CodonUsage()
{
Codon = CreateCodon(),
Frequency = 0.57f
};
return(GetOrCreate(() => codonUsage));
}
