hepatitis c virus ( hcv ) infection is a major cause of chronic hepatitis , liver cirrhosis and hepatocellular carcinoma worldwide .
the hcv genome is 9600 nt in length and carries a single , long open reading frame ( orf ) flanked by 5 and 3 non - translated regions .
the orf encodes a polyprotein of 3000 amino acids that is processed by cellular and viral proteases to yield at least 10 mature proteins : c , e1 , e2 , p7 , ns2 , ns3 , ns4a , ns4b , ns5a and ns5b ( 1,2 ) .
the sequence diversity among hcv genomes leads to the definition of a large number of subtypes distributed into six genotypes ( 3 ) .
in addition , hcv exists within its hosts as a pool of genetically distinct but closely related variants referred to as quasispecies ( 4 ) .
it is now well established that the genotype is a predictive factor of the response to interferon- therapy ( 5 ) . consequently
, intensive sequence analyses of hcv genomes are currently conducted , and > 40  000 nt sequences have been deposited to date into the ddbj / embl / genbank databases . in order to manage such large and growing collections of sequences , to facilitate sequence analysis and drug and vaccine design , several specialized databases have been developed ( 6 ) .
the database team members are involved in a network of experts for hcv nomenclature definition and harmonization ( 3 ) .
this database combines computer - annotated hcv sequences with protein three - dimensional ( 3d ) models and it is linked to numerous sequence and structure analysis tools on dedicated websites . the euhcvdb is mainly oriented towards the structural biology of hcv , including protein sequence , structure and function analyses ( 2 ) .
the euhcvdb is an extension of the french hcv database developed in 1999 ( 7 ) .
it is updated on a monthly basis from the embl nucleotide sequence database ( 8) and maintained in the postgresql relational database management system ( rdms ) . the programs for parsing the embl database flat files , annotating hcv entries , filling up and querying the database use sql and java .
great effort has been devoted to developing a fully automated annotation procedure using a reference set of 26 well - characterized complete hcv genomes representing 18 subtypes ( 3 ) .
the molecular models based protein homology are automatically computed and stored in a separate database by a protein molecular model database management system written in python and called modeome3d ( n. garnier , c. combet , c. geourjon , g. delage and e. bettler , manuscript in preparation ) .
the building procedure starts by the parsing of the embl database ( vrl section ) flat text file .
the second step of the procedure is the sequence annotation , which results in the creation of the euhcvdb and the euhcvdb3d databases by adding annotations to the embl data ( i.e. genome mapping , protein features , genotype / subtype or 3d models ) .
the sets of pre - computed multiple sequence alignments of complete proteins or reference genomes and 3d models are also updated monthly .
thus , the primary accession number , the creation date , the bibliographic references , the source feature and the sequence of each embl database entry are conserved in the euhcvdb entries .
the euhcvdb entry identifiers are built from the embl primary accession number to avoid any change in references for sequences .
a text search on the embl source feature is performed to retrieve subtype and isolate name of the deposited sequence .
the sequence of the entry is then retrieved and used to run a fasta ( 9 ) similarity search against the sequences of the reference genomes .
the annotations of the most similar genome are retrieved to map regions and features on the current sequence . the current entry is then subtyped by using two sets of reference nucleotide sequences as described in ( 3 ) .
these reference sequences cover two subgenomic regions , one in c / e1 and one in ns5b proteins , and are stored in two sequence databanks .
a fasta search is run for each sequence against each databank and the provisional genotype field of the entry is filled only if the following requirements are satisfied : sufficient coverage of the alignment , similarity level and consistency of genotype between the two subgenomic regions .
the annotation procedure ends by looking for protein 3d structural templates to build 3d models of the hcv proteins by homology modeling . for each sequence
, a similarity search is run against a selected set of hcv protein structures deposited in the protein data bank ( pdb ) ( 10 ) .
when acceptable alignments are found , the 3d models are computed using the geno3d program for automatic comparative homology modeling of proteins ( 11 ) . a product feature ( prod_ft qualifier ) indicated by model3d , which includes the template pdb code ,
is added to the corresponding mat_peptide feature of the entry and the 3d model is stored in the euhcvdb3d .
each euhcvdb entry offers external cross - references to the ncbi taxonomy , the uniprot knowledgebase ( uniprotkb ) ( 12 ) and to embl database , as well as internal cross - references to the reference genome used for annotation and to the euhcvdb3d molecular models .
the euhcvdb database is also cross - referenced by the uniprotkb / swiss - prot ( 12 ) and lanl hcv ( 13 ) databases and by the ncbi linkout system .
the automatic annotation procedure ensures standardized nomenclature for all entries across the database and builds a description of the hcv genomic regions and proteins that are included in the entry .
this procedure also provides bibliographic references , cross - references to external databases , genotype , well - characterized sites ( e.g. hypervariable region 1 , hvr1 ) or domains ( e.g. ns3 helicase ) , the source of the sequence ( e.g. isolate ) , and structural data as 3d protein models .
the protein annotations are done in close collaboration with the swiss - prot group of the swiss institute of bioinformatics .
the format and the controlled vocabulary of the uniprotkb / swiss - prot database are used in euhcvdb at the level of the prod_ft .
the static part allows the user to access the description of genomic regions or proteins by clicking on pictures ( figure 1a ) .
pre - computed multiple sequence alignments of reference genomes or complete protein sequences can be viewed and edited with the editalignment java applet developed in our team ( figure 1b ) . when the experimental 3d structures of the molecules are known , links to pdb files are available that allow users to view and analyze the structure using the jmol applet .
users can also find recommended nomenclature , the list of the reference genomes and links to other resources in the static part .
( b ) the multiple sequence alignment of ns3 protein from ( a ) viewed in the editalignment applet .
( c ) a query result page with the display and tools boxes , and list of hits .
( d ) an entry details page , with data for ns3 and links to the euhcvdb3d models .
( e ) a molecular model viewed through the euhcvdb3d interface . the jmol applet is linked with the alignment between the modeled and template pdb sequences . in the dynamic part , a query system ( not shown ) allows the building of dynamic sets of sequences or 3d models according to user - defined criteria ( > 30 different criteria can be defined ) and selected by the user through the query interface , e.g.  extract all the 3d models of the ns3 protease of confirmed genotype 3 , 4 and 5. the results ( figure 1c ) are displayed in a table where each row corresponds to an entry or a genomic region / protein that is described by a small set of identifiers and characteristics such as accession number , protein name , genotype , isolate , length and description .
a hypertext link on the accession number of each entry allows display of the complete entry data in the entry details page ( figure 1d ) .
this page contains hyperlinks to external resources such as embl database , to retrieve partial or complete nucleotide or protein sequences of the entry or to the jmol web page to analyze pre - computed 3d protein models when available ( figure 1e ) .
the results in figure 1c can be ordered by ascending / descending values of each column . above the table
, a form allows the user to change the number of results by page or to switch to a given page or accession number .
a toolbox is also available to export data ( e.g. sequences ) to other resources .
available sequence types are the full - length nucleotide sequence or the corresponding polyprotein , a genomic region or a protein , or a sequence corresponding to a polynucleotide or protein feature .
the toolbox allows the export of all / page/(un)selected results as a text file of entries , a pearson sequence file or a tab - delimited text file .
sequences can be transferred to the nps@ server ( 14 ) which is an integrated sequence analysis web server with a simple interface that provides the access to 46 programs for sequence analyses ( e.g. blast and clustal w ) and 12 biological databases . with the support of this server ,
the user can , for example , obtain a multiple sequence alignment of the full - length ns3 protein sequences to analyze the amino acid variability at each position of the alignment with the residue repertoire tool ( f. dorkeld , f. penin , g. delage and c. combet , unpublished data ) .
in addition , the 3d models of different variants can be extracted from the database and further analyzed using the pig web server for protein structure analysis ( n. garnier , g. delage and e. bettler , manuscript in preparation ) . selected 3d models
the user can interactively analyze the fitted models by using the jmol applet ( figure 1e ) that is dynamically linked to the corresponding sequence alignment . in this way , one can identify the differences between the variants . such analysis is helpful for a better understanding of structure  function relationships , which is of high relevance , e.g. for understanding drug resistance .
the user can also visualize the residue conservation at the model level , obtain a list of accessible residues , or detect ligand - binding or active sites using the sumo web server ( 15 ) .
the database has been running since march 2005 . the current release number 71 ( october 2006 ) comprises 43  124 entries and 646 protein 3d models representing 914 protein chains for a total of 383 443 residues and 2 930 254 atoms .
the relational database of annotated hcv sequences and protein 3d models we have developed focuses on hcv protein sequence , structure and function analyses . the automatic annotation process used to generate euhcvdb guarantees the consistency of annotations across the database , which allows efficient keyword searches and comprehensive sequence and structure analyses .
the euhcvdb website permits dynamic queries through a very simple interface , and query results can be further analyzed with a set of bioinformatics programs available in the nps@ and pig web servers . by providing the ability to conduct complex searches and analyses ,
moreover , we are working in an international collaborative effort with the us and japanese hcv databases to improve the use of harmonized hcv data and nomenclature , and making an effort to be as complementary as possible with the goal of providing helpful and efficient tools for hcv researchers around the world .
 the hepatitis c virus ( hcv ) genome shows remarkable sequence variability , leading to the classification of at least six major genotypes , numerous subtypes and a myriad of quasispecies within a given host . 
 a database allowing researchers to investigate the genetic and structural variability of all available hcv sequences is an essential tool for studies on the molecular virology and pathogenesis of hepatitis c as well as drug design and vaccine development . 
 we describe here the european hepatitis c virus database ( euhcvdb , ) , a collection of computer - annotated sequences based on reference genomes . 
 the annotations include genome mapping of sequences , use of recommended nomenclature , subtyping as well as three - dimensional ( 3d ) molecular models of proteins . 
 a www interface has been developed to facilitate database searches and the export of data for sequence and structure analyses . 
 as part of an international collaborative effort with the us and japanese databases , the european hcv database ( euhcvdb ) is mainly dedicated to hcv protein sequences , 3d structures and functional analyses . 
INTRODUCTION
DATABASE CONSTRUCTION
DATABASE CONTENTS
WEB INTERFACE
DATABASE STATISTICS
CONCLUSIONS