Project ROSALIND: Finding a Protein Motif

The following piece of code is an attempt to solve the "Finding a Protein Motif" puzzle from the Project Rosalind.

The input is a list of UniProt Protein Database access IDs. For each ID, the code reads the protein aminoacid sequence from the url in the form of http://www.uniprot.org/uniprot/uniprot_id.fasta. Then, for each protein, it searches for the N-glycosylation motif (a motif is a significant amino acid pattern), which is written as N{P}[ST]{P}. In this format, [X] means any aminoacid, and {X} means any amino acid except X.

The code properly handles overlaps, i.e. in the NMSNSSS string there are two overlapping substrings that satisfy the motif: NMSN and NSSS. The overlaps are not handled properly by the Regex.Matches method (some matches are missed), so some additional string manipulations were required.

The url http://prosite.expasy.org/scanprosite/ can be used to verify the output.

List<string> proteins = new List<string>();

string line;
using (StreamReader reader = new StreamReader("input.txt"))
{
 while ((line = reader.ReadLine()) != null)
 {
  proteins.Add(line);
 }
}

WebClient client = new WebClient();
Dictionary<string, string> proteinsDict = new Dictionary<string, string>();
foreach (string id in proteins)
{
 Stream stream = client.OpenRead("http://www.uniprot.org/uniprot/" + id + ".fasta");

 if (stream != null)
  using (StreamReader reader = new StreamReader(stream))
  {
   string protein = string.Empty;
   while ((line = reader.ReadLine()) != null)
   {
    if (!line.StartsWith(">"))
    {
     protein += line;
    }
   }

   proteinsDict.Add(id, protein);
  }
}

const string pattern = @"N[^P][ST][^P]";

using (StreamWriter writer = new StreamWriter("output.txt"))
{
 foreach (KeyValuePair<string, string> kvp in proteinsDict)
 {
  string val = kvp.Value;
  List<int> matches = new List<int>();
  int removed = 0;
  bool done = false;
  while (done == false)
  {
   Match match = Regex.Match(val, pattern);
   if(match.Success)
   {
    int index = val.IndexOf(match.Value);
    matches.Add(index + removed + 1);
    removed += index + 1;
    val = val.Substring(index + 1, val.Length - (index + 1));
   }
   else
   {
    done = true;
   }
  }

  if(matches.Count > 0)
  {
   string indices = string.Empty;
   writer.WriteLine(kvp.Key);
   indices = matches.Aggregate(indices, (current, index) => current + index + " ");
   writer.WriteLine(indices);
  }
 }
}

References

Finding a Protein Motif
My Profile at Project ROSALIND
by Evgeny. Also posted on my website