European Bioinformatics Institute EBI

Sequences of the genes/cDNAs can be retrieved from databases on the Internet at various web sites. For example, GeneBank (at the National Center for Biotechnology Information, NCBI) is at http //www.ncbi.nlm.nih.gov/ Web/Search/index.html. The EMBL Nucleotide Sequence database (through the European Bioinformatic Institute, EBI) can be found at http //www.ebi.ac.uk/queries/queries.html, whilst that of the DNA Data Bank of Japan is at http //www.ddbj.nig.ac.jp/. 

European Bioinformatics Institute (EBI) German Cancer Research Center (DKFZ) Stanford Microarray... 

The Swiss-Prot database is probably the most widely used protein database. It is maintained collaboratively by the European Bioinformatics Institute (EBI) and the Swiss Institute for Bioinformatics. It is relatively easy to access and search via the World Wide Web (Table 2.4). A sample entry for human insulin is provided in Figure 2.4. Additional information detailing such databases is available via the web addresses provided in Table 2.4 and in the bioinformatics publications listed at the end of this chapter. 

SWISS-PROT (Bairoch and Apweiler, 1999) is an annotated protein sequence database established in 1986 and maintained collaboratively by the Swiss Institute of Bioinformatics and the EMBL Outstation, The European Bioinformatics Institute (EBI). It strives to provide a high level of annotation, a minimal level of redundancy, a high level of... 

To make full use of microarray data it is necessary that data of published microarray experiments be made available to other researchers for comparison purposes. To this end, the Minimum Information About a Microarray Experiment (MIAME) (31) guidelines have been developed at the European Bioinformatics Institute (EBI). This standard describes the minimum information required to ensure that microarray data can be easily interpreted, and that results derived from its analysis can be independently verified. 

Other sequence databases can be found via the website (http //www.ebi.ac.uk/) of the European Bioinformatics Institute (EBI). Databanks managed by the EBI include ... 

Part of the EMBL, the European Bioinformatics Institute (EBI) is a centre for research and services in bioinformatics. The mission of the EBI is to ensure that information from molecular biology and genome research is placed in the public domain and is accessible freely to all facets of the scientific community. The Institute manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. 

One of the central activities of the European Bioinformatics Institute (EBI) (Emmert et ah, 1994) is development and distribution of the EMBL nucleotide sequence database (Stoesser et ah, 2001). This is a collaborative project with GenBank (NCBI, USA) and DDBJ (DNA database of Japan) to ensure that all the new and updated database entries are shared between the groups on a daily basis. The search of sequence databases and an access to various application tools can be approached from the home page of EBI at http //www.ebi.ac.uk/ (Figure 3.3). 

The European Bioinformatics Institute (EBI). This site is located at Hinxton Hall, Cambridge, UK. The home of the EMBL Nucleotide Sequence Database data management tools [including publicly accessible version of SRS—the Sequence Retrieval System (7)] protein family databases microarray tools etc. An extensive repository of resources for bioinformatics. 

Several public consortia, such as the European Bioinformatics Institute (EBI), the National Center for Biotechnical Information (NCBI), and many other organizations created databanks where data could be publicly submitted and described in a MIA ME-compI iant form. 

Universal Protein Knowledgebase (UniProt). European Bioinformatics Institute (EBI), Swiss Institute of Bioinformatics (SIB), Protein Information Resource (PIR), Georgetown Univ. URL http //www.uniprot.org. Central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. A central access point for extensive curated protein information, including function, classification, and cross-reference. 

In this paper we describe the basic design of a microarray gene expression database to help microarray users and their informatics teams set up their information services. The first version of the microarray database object model ArrayExpress, which is described here, was developed at the European Bioinformatics Institute (EBI) in collaboration with the German Cancer Research Centre (DKFZ) and posted on the Internet in November, 1999 (see (http //www.ebi.ac.uk/arrayexpress)). A relational database implementation maxd based on the ArrayExpress object model was conducted at the University of Manchester (http //bioinf.man.ac.uk/microarray/resources.html) and is widely used for microarray laboratory informatics support. 

FIGURE 6.3 An alignment of myoglobin and hemoglobin sequences generated by the ClustalW sequence alignment interface at the European Bioinformatics Institute (EBI) server (see Table 6.3). Residues are color coded by type. 

Like FASTA, BLAST has also been adapted to connect good diagonals and report local alignments with gaps. BLAST converts the database file into its own format to allow for faster reading. This makes it somewhat unwieldy to use in a local installation unless someone takes care of the installation. FASTA, on the other hand, is slower but easier to use. There exist excellent web servers that offer these programs, in particular at the National Center for Biotechnology Information (NCBI [59]) and at the European Bioinformatics Institute (EBI [60]) where BLAST or FASTA can be used on up-to-date DNA and protein databases. 

Protein databases used to be from direct protein sequencing, but now they are made almost exclusively from the translation of ORFs (Open Reading Frames on DNA sequences). Both the European Bioinformatics Institute (EBI) and National Center for Biotechnology Information (NCBI) provide databases, TREMBL [15] and GENPEPT [19] respectively, which are automatic translations from the CDS features of the DNA in their nucleotide databases. This includes some automated annotation of the role which the protein plays. 

The SRS 3D Viewer [28] is part of the SRS 3D server at the European Bioinformatics Institute (EBI) site (http //srs3d.ebi.ac.uk). Similar to Cn3D, SRS 3D is intuitive and easy to use. It enables the user to easily find all related structures, select one, and immediately see where the target sequence aligns onto the 3D structure (fig. 11.2B). Key differences between Cn3D and SRS 3D are that SRS 3D shows sequence features from the UniProt, InterPro, and PDB entries of the target sequence and enables users to easy map these features onto the structures (fig. 11.2C). SRS 3D also has a richer set of mouse and keyboard commands to help navigate and select parts of the sequence and structure. However, a drawback of the SRS 3D Viewer is that it can be difficult to install on some computers. SRS 3D is a commercial product but can be used freely via the Web to view any 3D structures in the PDB. 

The Radiation Hybrid Database (RHdb) is the central repository for all RH data. It is maintained at the European Bioinformatics Institute (EBI) in Cambridge, UK (Rodriguez-Tome and Lijnzaad, 2000). RHdb is a sophisticated Web- and FTP-based... 

Nucleotide sequences of nucleic acids can be retrieved from GenBank of the National Center for Biotechnology Information (NCBI) of the National Institute of Health (NIH) at http //www.ncbi.nhn.nih.gov/Genbank, European Bioinformatics Institute (EBI)... 

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