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Biological databases

Biological databases. Secuencia DNA. Secuencia Proteína. Reconocimiento. Estructura 3D. La vida real sin embargo….

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Biological databases

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  1. Biological databases

  2. Secuencia DNA Secuencia Proteína Reconocimiento Estructura 3D Genómica aplicada a la medicina clínica

  3. La vida real sin embargo… >gi|261252063|ref|NZ_ACZV01000005.1| Vibrioorientalis CIP 102891 VIA.Contig80, wholegenomeshotgunsequence ACGCGTTAAGTAGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAATGAATTGACGGGGGCCCGC ACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTACTCTTGACATCCAGAGA AGCCGGAAGAGATTCTGGTGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTG TTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTGTTTGCCAGCGAGTAATGTCGG GAACTCCAGGGAGACTGCCGGTGATAAACCGGAGGAAGGTGGGGACGACGTCAAGTCATCATGGCCCTTA CGAGTAGGGCTACACACGTGCTACAATGGCGCATACAGAGGGCAGCCAACTTGCGAAAGTGAGCGAATCC CAAAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCG TGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGG CTGCAAAAGAAGTAGGTAGTTTAACCTTCGGGAGAACGCTTACCACTTTGTGGTTCATGACTGGGGTGAA GTCGTAACAAGGTAGCCCTAGGGGAACCTGGGGCTGGATCACCTCCTTATACGATGATTACTCACGATGA GTGTCCACACAGATTGATATGTCTTTATTAGAGCTTTGAGGGGCTATAGCTCAGCTGGGAGAGCGCTTCG Secuencia Proteína Secuencia DNA ATOM 95 CE2 TRP 115 28.381 8.071 33.915 1.00 10.00 ATOM 96 CE3 TRP 115 27.500 9.825 32.526 1.00 10.00 ATOM 97 CZ2 TRP 115 27.750 7.155 33.103 1.00 10.00 ATOM 98 CZ3 TRP 115 26.888 8.895 31.705 1.00 10.00 ATOM 99 CH2 TRP 115 27.053 7.584 32.002 1.00 10.00 ATOM 100 N ASP 116 26.290 11.255 36.778 1.00 10.00 ATOM 101 CA ASP 116 25.763 10.825 38.096 1.00 10.00 ATOM 102 C ASP 116 24.689 11.802 38.607 1.00 10.00 ATOM 103 O ASP 116 24.564 12.103 39.797 1.00 10.00 ATOM 104 CB ASP 116 26.872 10.617 39.142 1.00 50.00 ATOM 105 CG ASP 116 26.368 10.397 40.557 1.00 50.00 ATOM 106 OD1 ASP 116 25.812 9.294 40.721 1.00 50.00 ATOM 107 OD2 ASP 116 26.590 11.276 41.416 1.00 50.00 ATOM 108 N PHE 117 23.915 12.348 37.709 1.00 10.00 ATOM 109 CA PHE 117 22.766 13.148 38.156 1.00 10.00 Estructura 3D Reconocimiento

  4. La cantidad de datos es enorme Genómica aplicada a la medicina clínica

  5. http://www3.ebi.ac.uk/Services/DBStats/

  6. Biological databases • Primary • Information comes fromexperiment • Databaseonlyorganizes and providesthe data • Ex.GenBank, EMBL • Derived • Annotateda posteriori • Data isrevised and corrected. Informationfromliteratureisadded • Ex.SWISS-PROT • Reusable Experimental data • GEO, SRA • Computationallyderived • Ex.PFAM • Specificissues Molecular Database Collection 2009 update

  7. Search strategies • Direct access to database • Usually more elaborated information • Global retrieval • Sequence Retrieval System (SRS), EBI-Eye, NCBI Entrez, MobyMiner • Automated, uniform. Allows to check several (all) databases simultaneously • Program access (bioXXX, Web services, Taverna)

  8. Origin of information • Individual research • Good quality but very limited amount • Massive sequencing projects: EST, HTS, genome projects. • Large amount of data. Quality not assured. Frequent update

  9. Main sequence repositories • DNA • EMBL, Genbank, DDBJ • Protein • Swissprot/TrEMBL, PIR

  10. Genómica aplicada a la medicina clínica

  11. Genómica aplicada a la medicina clínica

  12. TEXT

  13. Genómica aplicada a la medicina clínica

  14. Genómica aplicada a la medicina clínica

  15. Genómica aplicada a la medicina clínica

  16. Genómica aplicada a la medicina clínica

  17. Trusted annotation Translation from DNA http://www.expasy.org

  18. Cross links • Most database files contain links to other databases • DNA sequence to Protein sequence • Sequence to 3D structure • Sequence to bibliographic data • ....

  19. Warnings • Prediction method can fail and some times accurancy is not available • Prediction is always made of known issues • Databases can contain incorrect data • Avoid overvaloration of results

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