protected bool IsCleavablePosition(string sequence, int index, Proteases enzyme)
{
char s = char.ToUpper(sequence[index]);
switch (enzyme)
{
//cleaves peptides on the C-terminal side of lysine and arginine
case Proteases.Trypsin:
//proline residue is on the carboxyl side of the cleavage site
if (index < sequence.Length - 1 && char.ToUpper(sequence[index + 1]) == 'P')
{
return(false);
}
else if (s == 'K' || s == 'R')
{
return(true);
}
break;
//cuts after aromatic amino acids such as phenylalanine, tryptophan, and tyrosine.
case Proteases.Pepsin:
if (s == 'W' || s == 'F' || s == 'Y')
{
return(true);
}
break;
case Proteases.Chymotrypsin:
if (index < sequence.Length - 1 && char.ToUpper(sequence[index + 1]) == 'P')
{
return(false);
}
else if (s == 'W' || s == 'F' || s == 'Y')
{
return(true);
}
break;
case Proteases.GluC:
if (index < sequence.Length - 1 && char.ToUpper(sequence[index + 1]) == 'P')
{
return(false);
}
else if (s == 'E' || s == 'D')
{
return(true);
}
break;
default:
break;
}
return(false);
}
protected List <int> FindCutOffPosition(string sequence, Proteases enzyme)
{
//get cleavable position, make all possible peptide cutoff positoins
List <int> cutOffPosition = new List <int>();
cutOffPosition.Add(-1); //trivial to include starting place
for (int i = 0; i < sequence.Length; i++)
{
if (IsCleavablePosition(sequence, i, enzyme)) //enzyme
{
cutOffPosition.Add(i);
}
}
if (!IsCleavablePosition(sequence, sequence.Length - 1, enzyme))
{
cutOffPosition.Add(sequence.Length - 1); //trivial to include ending place
}
return(cutOffPosition);
}
public static List <string> Generate(string sequence,
Proteases enzyme, double missCleavage, double miniLength)
{
List <string> pepList = new List <string>();
List <int> cutOffPosition = FindCutOffPosition(sequence, enzyme);
//generate substring from sequences
int start, end;
for (int i = 0; i <= missCleavage; i++)
{
for (int j = 0; j < cutOffPosition.Count - i - 1; j++)
{
start = cutOffPosition[j] + 1;
end = cutOffPosition[j + 1 + i];
if (end - start + 1 >= miniLength) // put minimum length in place
{
pepList.Add(sequence.Substring(start, end - start + 1));
}
}
}
return(pepList);
}
public void SetProtease(Proteases enzyme)
{
this.enzyme = enzyme;
}
public GeneralPeptideGeneratorParameter(Proteases enzyme, int missCleavage = 2, int miniLength = 7)
{
this.enzyme = enzyme;
this.missCleavage = missCleavage;
this.miniLength = miniLength;
}
public GeneralPeptideGeneratorParameter()
{
enzyme = Proteases.Trypsin;
missCleavage = 2;
miniLength = 7;
}
public void SetProtease(Proteases enzyme)
{
enzyme_ = enzyme;
}
public ProteinDigest(int missCleavage, int minLength, Proteases enzyme)
{
miss_cleavage_ = missCleavage;
min_length_ = minLength;
enzyme_ = enzyme;
}
