[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
[email protected]://pbil.ibcp.fr 2
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/
[email protected]://pbil.ibcp.fr 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
[email protected]://pbil.ibcp.fr 6
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
[email protected]://pbil.ibcp.fr 17
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)
[email protected]://pbil.ibcp.fr 19
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
http://euhcvdb.ibcp.fr
[email protected]://pbil.ibcp.fr 20
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