hcv test case for embrace c. charavay, d. crisan, d. grando, c. geourjon,

[email protected]://pbil.ibcp.fr 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 ProtéinesBioinformatique et RMN structurales

Pôle BioInformatique de LyonIFR128 BioSciences Lyon-Gerland

UMR 5086 CNRS- UCBL7, passage du Vercors

69367 Lyon CEDEX 07 - FRANCE

http://www.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://euhcvdb.ibcp.fr

http://www.virgil-net.org/ http://hepcvax.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


Home pagehttp://euhcvdb.ibcp.fr


Annotationhttp://euhcvdb.ibcp.fr

EMBLdatabaseflat files Parser

DAO (JDBC)DTO euhcvdb_embl

DAO (JDBC) DTO DTO

cloneDTO entry euhcvdb

Web interface

(JSP, servlets, DAO, DTO,

Parser)

HCV Annotate

DTO reference

DAO (JDBC)

euhcvdb_ref

DAO (JDBC)

C/E1 fasta seqsNS5B

fasta seqs


Relational schemahttp://euhcvdb.ibcp.fr


Home pagehttp://euhcvdb.ibcp.fr


Static resources : NS3http://euhcvdb.ibcp.fr



Static resources : NS3



Dynamic query : query page


Dynamic query: results pagehttp://euhcvdb.ibcp.fr


Entry detailshttp://euhcvdb.ibcp.fr


Dynamic query: results pagehttp://euhcvdb.ibcp.fr


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


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

America27,1%

Asia10,7%

Europe34,7%

France24,7%

Africa1,2%

Oceania1,7%

487

1133

17012146

2526

3248

5074

6728

0

1000

2000

3000

4000

5000

6000

7000

8000

1998 1999 2000 2001 2002 2003 2004 2005

133801547366

1169926

1953285

2875372

6934007

5918042

4061064

0

1000000

2000000

3000000

4000000

5000000

6000000

7000000

8000000

1998 1999 2000 2001 2002 2003 2004 2005

http://npsa-pbil.ibcp.fr

• 46 algorithms (BLAST, CLUSTALW)• 12 databases• PBIL, ExpASy, PDB,…

• EMBRACE -> GPS@ (Dr C. BLANCHET)


Tools: Numberhttp://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



The teamhttp://euhcvdb.ibcp.fr

C. CharavayHepCVax

D. CRISANHepCVax

D. GRANDOVIRGIL

Dr C.GEOURJONCNRS

Dr. F. PENINCNRS

Pr. G. DELEAGEUCBL

Dr. C. COMBETCNRS Dr C.BLANCHET

CNRS

hcv test case for embrace c. charavay, d. crisan, d. grando, c. geourjon,

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