1 / 20

HCV test case for EMBRACE C. Charavay, D. Crisan, D. Grando, C. Geourjon,

HCV test case for EMBRACE C. Charavay, D. Crisan, D. Grando, C. Geourjon, F. Penin, G. Deléage and C. Combet . I nstitut de B iologie et C himie des P rotéines Bioinformatique et RMN structurales Pôle BioInformatique de Lyon IFR128 BioSciences Lyon-Gerland UMR 5086 CNRS- UCBL

noleta
Download Presentation

HCV test case for EMBRACE C. Charavay, D. Crisan, D. Grando, C. Geourjon,

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. HCV test case for EMBRACE C. Charavay, D. Crisan, D. Grando, C. Geourjon, F. Penin, G. Deléage and C. Combet. Institut de Biologie et Chimie des Protéines Bioinformatique et RMN structurales Pôle BioInformatique de Lyon IFR128 BioSciences Lyon-Gerland UMR 5086 CNRS- UCBL 7, passage du Vercors 69367 Lyon CEDEX 07 - FRANCE http://www.ibcp.fr

  2. http://euhcvdb.ibcp.fr A long story… • 1999-2005 HCVDB: • Aim: analysis of correlations between sequence and clinical (genotype vs phenotype) • Results: 53 releases / no clinical data • 2005-… euHCVdb: EU FP5 HepCVax - EU FP6 VIRGIL NoE • focus on protein sequence, structure and function analyses and structural biology of HCV • Improved information technology • Improved sequence annotations • Integration of clinical data • Integration of protein structural data in order to understand at molecular level resistance to drugs http://hepcvax.ibcp.fr/ http://www.virgil-net.org/

  3. http://euhcvdb.ibcp.fr http://www.virgil-net.org/ • Network of excellence of 6th framework program (started 1st may 2004) • 9 M€ / 4 years • 55 organizations of 12 countries (>60 academic labs / 7 companies) • Focusing on comprehensively covering the problem of viral resistance (HCV, HBV and Influenza) • 7 platforms: • SURVEIL: surveillance system • CLINVIR: monitoring of clinical trials / characterization of resistance • MODELS: assessment of antiviral drug resistance / understand mechanism • HOST: host determinant factors involved in resistance • DRUGPHARM: pharmacological approach to treatment failure • INNOTECH: key technologies and methodologies • IMPACT: societal impact of drug resistance

  4. http://euhcvdb.ibcp.fr

  5. Home page http://euhcvdb.ibcp.fr

  6. Annotation http://euhcvdb.ibcp.fr C/E1 fasta seqs NS5B fasta seqs EMBL database flat files DAO(JDBC) DAO(JDBC) DTO clone DAO (JDBC) DTO entry Parser DTO DTO euhcvdb_embl euhcvdb HCV Annotate DTO reference Web interface (JSP, servlets, DAO, DTO, Parser) DAO (JDBC) euhcvdb_ref

  7. Relational schema http://euhcvdb.ibcp.fr

  8. Home page http://euhcvdb.ibcp.fr

  9. Static resources : NS3 http://euhcvdb.ibcp.fr

  10. Static resources : NS3 http://euhcvdb.ibcp.fr

  11. Dynamic query : query page http://euhcvdb.ibcp.fr

  12. Dynamic query: results page http://euhcvdb.ibcp.fr

  13. Entry details http://euhcvdb.ibcp.fr

  14. Entry details http://euhcvdb.ibcp.fr

  15. Dynamic query: results page http://euhcvdb.ibcp.fr

  16. Tools: NPS@ http://euhcvdb.ibcp.fr

  17. Tools: NPS@ http://euhcvdb.ibcp.fr • http://npsa-pbil.ibcp.fr • 46 algorithms (BLAST, CLUSTALW) • 12 databases • PBIL, ExpASy, PDB,… • EMBRACE -> GPS@ (Dr C. BLANCHET)

  18. Tools: Number http://euhcvdb.ibcp.fr

  19. http://euhcvdb.ibcp.fr Concluding remarks • Improved annotation algorithms • Follow recommended nomenclature (Heidelberg nomenclature meeting) • Integration of 3D data for complete CDS (extension to other entries) • Finalize undergoing developments (3D analysis tools, HCV tools) • International collaborative effort with the japanese and Los Alamos HCV databases and UniProt database (cross-reference) • Clinical data • EMBRACE: monthly update of genomic/proteins of HCV multiple sequence alignments

  20. http://euhcvdb.ibcp.fr The team Dr. F. PENIN CNRS Pr. G. DELEAGE UCBL Dr. C. COMBET CNRS Dr C.BLANCHET CNRS D. CRISAN HepCVax D. GRANDO VIRGIL Dr C.GEOURJON CNRS C. Charavay HepCVax

More Related