biological databases

Biological databases

Secuencia DNA Secuencia Proteína

Estructura 3DReconocimiento14/10/2009

Genómica aplicada a la medicina clínica 2

La vida real sin embargo…>gi|261252063|ref|NZ_ACZV01000005.1| Vibrio orientalis CIP 102891 VIA.Contig80, whole genome shotgun sequence ACGCGTTAAGTAGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAATGAATTGACGGGGGCCCGC ACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTACTCTTGACATCCAGAGA AGCCGGAAGAGATTCTGGTGTGCCTTCGGGAACTCTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTG TTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTGTTTGCCAGCGAGTAATGTCGG GAACTCCAGGGAGACTGCCGGTGATAAACCGGAGGAAGGTGGGGACGACGTCAAGTCATCATGGCCCTTA CGAGTAGGGCTACACACGTGCTACAATGGCGCATACAGAGGGCAGCCAACTTGCGAAAGTGAGCGAATCC CAAAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCG TGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGG CTGCAAAAGAAGTAGGTAGTTTAACCTTCGGGAGAACGCTTACCACTTTGTGGTTCATGACTGGGGTGAA GTCGTAACAAGGTAGCCCTAGGGGAACCTGGGGCTGGATCACCTCCTTATACGATGATTACTCACGATGA GTGTCCACACAGATTGATATGTCTTTATTAGAGCTTTGAGGGGCTATAGCTCAGCTGGGAGAGCGCTTCG

ATOM 95 CE2 TRP 115 28.381 8.071 33.915 1.00 10.00ATOM 96 CE3 TRP 115 27.500 9.825 32.526 1.00 10.00ATOM 97 CZ2 TRP 115 27.750 7.155 33.103 1.00 10.00ATOM 98 CZ3 TRP 115 26.888 8.895 31.705 1.00 10.00ATOM 99 CH2 TRP 115 27.053 7.584 32.002 1.00 10.00ATOM 100 N ASP 116 26.290 11.255 36.778 1.00 10.00ATOM 101 CA ASP 116 25.763 10.825 38.096 1.00 10.00ATOM 102 C ASP 116 24.689 11.802 38.607 1.00 10.00ATOM 103 O ASP 116 24.564 12.103 39.797 1.00 10.00ATOM 104 CB ASP 116 26.872 10.617 39.142 1.00 50.00ATOM 105 CG ASP 116 26.368 10.397 40.557 1.00 50.00ATOM 106 OD1 ASP 116 25.812 9.294 40.721 1.00 50.00ATOM 107 OD2 ASP 116 26.590 11.276 41.416 1.00 50.00ATOM 108 N PHE 117 23.915 12.348 37.709 1.00 10.00ATOM 109 CA PHE 117 22.766 13.148 38.156 1.00 10.00

Secuencia DNA Secuencia Proteína

Estructura 3DReconocimiento

La cantidad de datos es enorme

14/10/2009Genómica aplicada a la medicina

clínica 4

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

Biological databases

Primary Information comes from experiment Database only organizes and provides the data Ex. GenBank, EMBL

Derived Annotated a posteriori Data is revised and corrected. Information from

literature is added Ex. SWISS-PROT

Reusable Experimental data GEO, SRA

Computationally derived Ex. PFAM

Specific issues

Molecular Database Collection 2009 update

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)

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

Main sequence repositories

DNA EMBL, Genbank, DDBJ

Protein Swissprot/TrEMBL, PIR

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Trusted annotation

Translation from DNA

http://www.expasy.org

Cross links

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

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