Dense Alu clustering and a potential new member of the NF kappa B family within a 90 kilobase HLA class III segment.

We have conducted a detailed structural analysis of 90 kilobases (kb) of the HLA Class III region from the Bat2 gene at the centromeric end to 23 kb beyond TNF. A single contig of 80 kb was sequenced entirely with a group of four smaller contigs covering 10 kb being only partly sequenced. This region contains four known genes and a novel telomeric potential coding region. The genes are bracketed by long, dense clusters of Alu repeats belonging to all the major families. At least six new families of MER repeats and one pseudogene are intercalated within and between the Alu clusters. The most telomeric 3.8 kb contains three potential exons, one of which bears strong homology to the ankyrin domain of the DNA binding factors NF kappa B and I kappa B.

A radiation hybrid transcript map of the mouse genome.

Expressed-sequence tag (EST) maps are an adjunct to sequence-based analytical methods of gene detection and localization for those species for which such data are available, and provide anchors for high-density homology and orthology mapping in species for which large-scale sequencing has yet to be done. Species for which radiation hybrid-based transcript maps have been established include human, rat, mouse, dog, cat and zebrafish. We have established a comprehensive first-generation-placement radiation hybrid map of the mouse consisting of 5,904 mapped markers (3,993 ESTs and 1,911 sequence-tagged sites (STSs)). The mapped ESTs, which often originate from small-EST clusters, are enriched for genes expressed during early mouse embryogenesis and are probably different from those localized in humans. We have confirmed by in situ hybridization that even singleton ESTs, which are usually not retained for mapping studies, may represent bona fide transcribed sequences. Our studies on mouse chromosomes 12 and 14 orthologous to human chromosome 14 show the power of our radiation hybrid map as a predictive tool for orthology mapping in humans.

A radiation hybrid map of mouse genes.

A comprehensive gene-based map of a genome is a powerful tool for genetic studies and is especially useful for the positional cloning and positional candidate approaches. The availability of gene maps for multiple organisms provides the foundation for detailed conserved-orthology maps showing the correspondence between conserved genomic segments. These maps make it possible to use cross-species information in gene hunts and shed light on the evolutionary forces that shape the genome. Here we report a radiation hybrid map of mouse genes, a combined project of the Whitehead Institute/Massachusetts Institute of Technology Center for Genome Research, the Medical Research Council UK Mouse Genome Centre, and the National Center for Biotechnology Information. The map contains 11,109 genes, screened against the T31 RH panel and positioned relative to a reference map containing 2,280 mouse genetic markers. It includes 3,658 genes homologous to the human genome sequence and provides a framework for overlaying the human genome sequence to the mouse and for sequencing the mouse genome.

A gene map of the human genome.

The human genome is thought to harbor 50,000 to 100,000 genes, of which about half have been sampled to date in the form of expressed sequence tags. An international consortium was organized to develop and map gene-based sequence tagged site markers on a set of two radiation hybrid panels and a yeast artificial chromosome library. More than 16,000 human genes have been mapped relative to a framework map that contains about 1000 polymorphic genetic markers. The gene map unifies the existing genetic and physical maps with the nucleotide and protein sequence databases in a fashion that should speed the discovery of genes underlying inherited human disease. The integrated resource is available through a site on the World Wide Web at http://www.ncbi.nlm.nih.gov/SCIENCE96/.

A physical map of 30,000 human genes.

A map of 30,181 human gene-based markers was assembled and integrated with the current genetic map by radiation hybrid mapping. The new gene map contains nearly twice as many genes as the previous release, includes most genes that encode proteins of known function, and is twofold to threefold more accurate than the previous version. A redesigned, more informative and functional World Wide Web site (www.ncbi.nlm.nih.gov/genemap) provides the mapping information and associated data and annotations. This resource constitutes an important infrastructure and tool for the study of complex genetic traits, the positional cloning of disease genes, the cross-referencing of mammalian genomes, and validated human transcribed sequences for large-scale studies of gene expression.

RHdb: the Radiation Hybrid database.

Since July 1995, the European Bioinformatics Institute (EBI) has maintained RHdb (http://www.ebi.ac.uk/RHdb), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. RHdb is also served by CORBA servers. The EBI is an Outstation of the European Molecular Biology Laboratory (EMBL).

EBI databases and services.

The EMBL Outstation-European Bioinformatics Institute (EBI) is a center for research and services in bioinformatics. It serves researchers in molecular biology, genetics, medicine, and agriculture from academia, and the agricultural, biotechnology, chemical, and pharmaceutical industries. The Institute manages and makes available databases of biological data including nucleic acid, protein sequences, and macromolecular structures. It provides to this community bioinformatics services relevant to molecular biology free of charge over the Internet. Some of these databases and services are described in this review.

The BioCatalog.

MOTIVATION: The BioCatalog is a database of information on software of interest in molecular biology and genetics. The programs are grouped by domain of interest. AVAILABILITY: The BioCatalog is freely distributed as ASCII files. It can be searched through its Web interface at http://www.ebi.ac.uk/biocat. CONTACT: biocat@ebi. ac.uk

The Radiation Hybrid Database.

Since July 1995, the European Bioinformatics Institute (EBI) has maintained RHdb, a public database for radiation hybrid data. Radiation hybrid data are used in the generation of alternative genetic maps as they can include non-polymorphic markers and are also powerful enough to order unresolved genetic clusters of polymorphic STSs. The EBI is an Outstation of the European Molecular Biology Laboratory (EMBL).

JESAM: CORBA software components to create and publish EST alignments and clusters.

MOTIVATION: Expressed Sequence Tags (ESTs) are cheap, easy and quick to obtain relative to full genomic sequencing and currently sample more eukaryotic genes than any other data source. They are particularly useful for developing Sequence Tag Sites (STSs for mapping), polymorphism discovery, disease gene hunting, mass spectrometer proteomics, and most ironically for finding genes and predicting gene structure after the great effort of genomic sequencing. However, ESTs have many problems and the public EST databases contain all the errors and high redundancy intrinsic to the submitted data so it is often found that derived database views, which reduce both errors and redundancy, are more effective starting points for research than the original raw submissions. Existing derived views such as EST cluster databases and consensus databases have never published supporting evidence or intermediary results leading to difficulties trusting, correcting, and customizing the final published database. These difficulties have lead many groups to wastefully repeat the complex intermediary work of others in order to offer slightly different final views. A better approach might be to discover the most expensive common calculations used by all the approaches and then publish all intermediary results. Given a globally accessible database with a suitable component interface, like the JESAM software described in this paper, the creation of customized EST-derived databases could be achieved with minimum effort. RESULTS: Databases of EST and full-length mRNA sequences for four model organisms have been self-compared by searching for overlaps consistent with contiguity. The sequence comparisons are performed in parallel using a PVM process farm and previous results are stored to allow incremental updates with minimal effort. The overlap databases have been published with CORBA interfaces to enable flexible global access as demonstrated by example Java applet browsers. Simple cDNA supercluster databases built as alignment database clients are themselves published via CORBA interfaces browsable with prototypical applets. A comparison with UniGene Mouse and Rat databases revealed undesirable features in both and the advantages of contrasting perspectives on complex data. AVAILABILITY: The software is packaged as two Jar files available from: URL: http://corba.ebi.ac.uk/EST/jesam/jesam. html. One jar contains all the Java source code, and the other contains all the C, C++ and IDL code. Links to working examples of the alignment and cluster viewers (if remote firewall permits) can be found at http://corba.ebi.ac.uk/EST. All the Washington University mouse EST traces are available for browsing at the same URL.

RHdb: the radiation hybrid database.

Since July 1995, the European Bioinformatics Institute (EBI) has maintained RHdb (http://www.ebi.ac.uk/RHdb ), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. RHdb is also served by CORBA servers. The EBI is an Outstation of the European Molecular Biology Laboratory (EMBL).

The radiation hybrid database.

Since July 1995, the European Bioinformatics Institute (EBI) has maintained the Radiation Hybrid database (RHdb; http://www.ebi.ac. uk/RHdb ), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. Recently, CORBA access has been added to RHdb. The EBI is an Outstation of the European Molecular Biology Laboratory (EMBL).

Mapplet: a CORBA-based genome map viewer.

MOTIVATION: There are a large number of genetic and physical maps, distributed at many sites. Each site offers different kinds of access methods and viewers. CORBA, the de facto standard for distributed object-oriented computing, offers new opportunities to unify the view on these maps through standard interfaces. A collaboration of Infobiogen and the EBI proposes a common IDL for maps. RESULTS: A CORBA map viewer is presented which serves as a proof of concept for the proposed IDL. It demonstrates its usefulness in the context of map viewing and its ability to handle large maps with <1000 markers. The viewer gives access to the maps of the Radiation Hybrid Database at EBI. It gives a quick overview of several large maps side by side. The marker density at each map position is displayed and different marker types can be highlighted. AVAILABILITY: Demonstration and source code at: http://sunny.ebi.ac.uk/ approximately jungfer/Mapplet CONTACT: jungfer@ebi.ac.uk

A CORBA server for the Radiation Hybrid DataBase.

Modern biology depends on a wide range of software interacting with a large number of data sources, varying both in size, complexity and structure. The range of important databases in molecular biology and genetics makes it crucial to overcome the problems which this multiplicity presents. At EMBL-EBI we have started to use CORBA technology to support interoperability between a variety of databases, as well as to facilitate the integration of tools that access these databases. Within the Radiation Hybrid DataBase project we are confronted daily with the interoperation and linking issues. In this paper we present a CORBA infrastructure implemented to access the Radiation Hybrid DataBase.

GBuilder--an application for the visualization and integration of EST cluster data.

This paper presents a network-centric DNA sequence visualization and analysis tool called GBuilder. The tool is an easy-to-use Java application that can be used to analyze DNA sequence clusters and assemblies. The emphasis is on the analysis of EST data, where these highly redundant collections of low-quality and often alternatively spliced or chimeric sequence data are difficult to explore. The tool has the capacity to visualize similarities or dissimilarities between sequences at the level of the nucleotide base or annotation in many ways. Sequences may also be edited manually. The novel feature of GBuilder is its ability to access different data sources and analysis applications available on the Internet and to integrate these results and functionality back into itself. External resources such as EST cluster databases and conventional command-line analysis applications are integrated and accessed using CORBA (Common Object Request Broker Architecture), which provides a standard implementation independent protocol for integration. New CORBA services can be integrated immediately if they use a known interface described using the Interface Definition Language.

The Radiation Hybrid Database.

Since July 1995, the European Bioinformatics Institute (EBI) has maintained RHdb (http://www.ebi.ac.uk/RHdb/RHdb.html ), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. Recently, CORBA access has been added to Rhdb. The EBI is an Outstation of the European Molecular Biology Laboratory (EMBL).

Accessing and distributing EMBL data using CORBA (common object request broker architecture).

BACKGROUND: The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. RESULTS: A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. CONCLUSIONS: The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems.

IARC p53 mutation database: a relational database to compile and analyze p53 mutations in human tumors and cell lines. International Agency for Research on Cancer.

The tumor suppressor p53 gene is the most frequently mutated gene in human cancer. To date, more than 10,000 mutations have been described in the literature, and these data are available in various electronic formats on the World Wide Web. Here we describe the structure and format of the different p53 datasets maintained and curated at the International Agency for Research on Cancer (IARC) in Lyon, France. These include p53 somatic mutations (more than 10,000 entries), p53 germline mutations (144 entries), and p53 polymorphisms (13 entries), with the somatic mutations organized into a relational database using AccessTM. The main features of these datasets are (1) controlled entry with standardized format and restricted vocabulary, (2) inclusion of annotations on individual characteristics and exposures, and (3) a classification of pathologies based on the International Classification of Diseases for Oncology (ICD-O). In addition, several interfaces have been developed to analyze the data in order to produce mutation spectra, codon analyses, or visualization of the mutation with the tertiary structure of the protein. All datasets and tools for analysis are available at http://www.iarc.fr/p53/homepage.