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 <Operon> GetOperons(List <GeneInfo> GeneInfoList) { List <Operon> Operons = new List <Operon>(); foreach (GeneInfo G in GeneInfoList) { Console.WriteLine("Getting operon info for: " + G.GeneName); Operons.Add(Operon_Mgt.FindOperon(G.OrganizmName, G.OrganizmAlias, G.GeneName));//"Escherichia coli K-12 MG1655", "eco", "metL")); } Operon_Mgt.SerializeOperons(@"C:\deleteme\Operons.txt", Operons); //Operons = Operon_Mgt.DeserializeOperons(@"C:\deleteme\Operons.txt"); return(Operons); }
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(); }