/// <summary>
/// Translate the coding sequence of a transcript
/// </summary>
/// <param name="transcript"></param>
/// <returns></returns>
public static ISequence OneFrameTranslation(ISequence dnaSequence, bool mitochondrial)
{
ISequence rnaSequence = Transcription.Transcribe(dnaSequence);
ISequence proteinSequence;
if (!mitochondrial)
{
proteinSequence = ProteinTranslation.Translate(rnaSequence);
}
else
{
List <byte> aminoAcidSequence = new List <byte>();
for (int codonNum = 0; codonNum < (int)(rnaSequence.Count / 3); codonNum++)
{
// Check for start codon, and add 'M' if so
if (aminoAcidSequence.Count == 0 &&
CodonsVertebrateMitochondrial.START_CODONS.Contains(
new string(dnaSequence.GetSubSequence(codonNum * 3, GeneModel.CODON_SIZE).Select(bp => (char)bp).ToArray())))
{
aminoAcidSequence.Add((byte)CodonsVertebrateMitochondrial.DEFAULT_START_AA);
continue;
}
aminoAcidSequence.Add(CodonsVertebrateMitochondrial.TryLookup(rnaSequence, codonNum * 3, out byte aa) ? aa : (byte)'X');
}
proteinSequence = new Sequence(Alphabets.AmbiguousProtein, aminoAcidSequence.ToArray());
}
return(proteinSequence);
}
/// <summary>
/// Translate 3 byte representations of DNA bases to an amino acid
/// </summary>
/// <param name="mitochondrial"></param>
/// <param name="base1"></param>ec
/// <param name="base2"></param>
/// <param name="base3"></param>
/// <param name="aminoAcid"></param>
/// <returns></returns>
public static bool TryTranslateBytes(bool mitochondrial, byte base1, byte base2, byte base3, out byte aminoAcid)
{
if (mitochondrial)
{
return(CodonsVertebrateMitochondrial.TryLookup(
Transcription.GetRnaComplement(base1),
Transcription.GetRnaComplement(base2),
Transcription.GetRnaComplement(base3),
out aminoAcid));
}
else
{
return(Codons.TryLookup(
Transcription.GetRnaComplement(base1),
Transcription.GetRnaComplement(base2),
Transcription.GetRnaComplement(base3),
out aminoAcid));
}
}
