public static void GetGeneOrtologSequences()
{
//lysC = K00928 (ortholog list)
//http://rest.kegg.jp/link/genes/K00928
List <string> Species = new List <string>();
Species.Add("eco");
Species.Add("ppf"); // pseudomonada putida f1
Species.Add("noc"); // Nitrosococcus oceani
Species.Add("vco"); // Vibrio cholerae O395
Species.Add("ype"); // Yersinia pestis CO92
Species.Add("asu"); // Actinobacillus succinogenes
Species.Add("son"); // Shewanella oneidensis
Species.Add("acd"); // Acinetobacter oleivorans
Species.Add("rma"); // Candidatus Ruthia magnifica
string OrthologList = KEGG_Mgt.GetOrthologList("K00928");
List <string> GeneNames = KEGG_Mgt.GetGeneNamesFromOrthologList(Species, OrthologList);
List <GeneInfo> GeneInfoList = KEGG_Mgt.GetGeneInfoByKEGGGenes(Species, GeneNames);
List <Operon> Operons = Operon_Mgt.GetOperons(GeneInfoList);
List <string> DNASequences = KEGG_Mgt.GetFastaDNASequencesByOperons(Operons, GeneInfoList);
foreach (string Fasta in DNASequences)
{
Console.WriteLine(Fasta);
}
Console.ReadKey();
}
public static List <string> GetFastaDNASequencesByOperons(List <Operon> Operons, List <GeneInfo> GeneInfoList)
{
List <string> DNASequences = new List <string>();
for (int I = 0; I < GeneInfoList.Count; I++)
{
if (Operons[I].Strand == 1)
{
DNASequences.Add(
KEGG_Mgt.AddFastaDescription(
KEGG_Mgt.GetCutSequence(
Operons[I].PosLeft - 200, Operons[I].PosLeft, 1, GeneInfoList[I].Chr, GeneInfoList[I].OrganizmAlias),
GeneInfoList[I]));
}
else
{
DNASequences.Add(
KEGG_Mgt.AddFastaDescription(
KEGG_Mgt.GetCutSequence(
Operons[I].PosRight, Operons[I].PosRight + 200, 2, GeneInfoList[I].Chr, GeneInfoList[I].OrganizmAlias),
GeneInfoList[I]));
}
}
SerializeFasta(@"C:\deleteme\Fasta.txt", DNASequences);
//DNASequences = DeserializeFasta(@"C:\deleteme\Fasta.txt");
return(DNASequences);
}
public static void GetPathwaySequences()
{
// genes:
// http://rest.kegg.jp/link/genes/enzyme:2.7.2.4/
// ortologs:
// http://www.kegg.jp/kegg-bin/show_pathway?ko00270
// Enzymes EC No
List <string> ECList = new List <string>();
ECList.Add("4.4.1.1");
ECList.Add("2.5.1.48");
ECList.Add("2.3.1.46");
ECList.Add("2.7.2.4");
ECList.Add("1.2.1.11");
ECList.Add("1.1.1.3");
ECList.Add("2.3.1.31");
ECList.Add("4.2.1.22");
ECList.Add("4.4.1.8");
ECList.Add("2.5.1.49");
ECList.Add("2.1.1.5");
ECList.Add("2.1.1.10");
ECList.Add("2.1.1.13");
ECList.Add("2.1.1.14");
string Organizm = "eco"; // ece = ecoli / hum = hsa
List <string> KEGGGenes = KEGG_Mgt.GetKEGGGenesIDs(Organizm, ECList);
List <GeneInfo> GeneInfoList = KEGG_Mgt.GetGeneInfoByKEGGGenes(Organizm, KEGGGenes);
List <Operon> Operons = Operon_Mgt.GetOperons(GeneInfoList);
List <string> DNASequences = KEGG_Mgt.GetFastaDNASequencesByOperons(Operons, GeneInfoList);
foreach (string Fasta in DNASequences)
{
Console.WriteLine(Fasta);
}
Console.ReadKey();
}