Exemple #1
0
        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);
        }
Exemple #3
0
        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();
        }