XEMBL: distributing EMBL data in XML format

Data in the EMBL Nucleotide Sequence Database is traditionally available in a flat file format that has a number of known shortcomings. With XML rapidly emerging as a standard data exchange format that can address some problems of flat file formats by defining data structure and syntax, there is now a demand to distribute EMBL data in an XML format. XEMBL is a service tool that employs CORBA servers to access EMBL data, and distributes the data in XML format via a number of mechanisms. AVAILABILITY: Use of the XEMBL service is free of charge at http://www.ebi.ac.uk/xembl/, and can be accessed via web forms, CGI, and a SOAP-enabled service. SUPPLEMENTARY INFORMATION: Information on the EMBL Nucleotide Sequence Database is available at http://www.ebi.ac.uk/embl/. The EMBL Object Model is available at http://corba.ebi.ac.uk/models/. Information on the EMBL CORBA servers is at http://corba.ebi.ac.uk/     

New head in Heidelberg. [interview by Graham Tebb

This spring, Iain Mattaj will become the new Director General of the European Molecular Biology Laboratory (EMBL). Graham Tebb talks with him about his research career, his plans for his own future and that of the EMBL.     

Cw * 1505: a novel HLA-C allele isolated from a B * 7301 haplotype

The nucleotide sequence data reported in this paper have been submitted to the EMBL database and have been assigned the accession number X78343. The name Cw ^*1505 was officially assigned by the WHO Nomenclature Committee in May 1994. This follows the agreed policy that, subject to the conditions stated in the most recent Nomenclature Report (The WHO Nomenclature Committee 1992), names will be assigned to new sequences as they are identified. Lists of such new names will be published in he following WHO Nomenclature Report     

DPB1 * BR: an Mhc class II DPB1 allele (DPB1 * 6601) of negroid origin

The nucleotide sequence data reported in this paper have been submitted to the EMBL nucleotide sequence database and have been assigned the accession number X96986. The nameDPB1 ^* 6601 was officially assigned by the WHO Nomenclature Committee in May 1996. This follows the agreed policy that, subject to the conditions stated in the most recent Nomenclature Report (Bodmer et al. 1995), names will be assigned to new sequences as they are identified. Lists of such sequences will be published in the following WHO Nomenclature Report     

Sequencing of a new HLA-B41 subtype (B * 4102) that occurs with a high frequency in the Caucasoid population

The nucleotide sequence data reported in this paper have been submitted to the EMBL database and have been assigned the accession number X81363. The name B ^* 4102 was officially assigned by the WHO Nomenclature Committee in November 1994. This follows the agreed policy that, subject to the conditions stated in the most recent Nomenclature Report (Bodmer et al. 1994), names will be assigned to new sequence as they are identified. Lists of such new names will be published in the following WHO Nomenclature Report     

Mapping new EMBL-derived barley microsatellites and their use in differentiating German barley cultivars

By searching the EMBL DNA sequence database, we were able to develop 39 new, database-derived barley microsatellites. Eighteen of these EMBL microsatellites were mapped either to the interspecific barley map Lerche×BGRC41936 (L×41), the Igri×Franka map (I×F, Graner et al. 1991), or to both maps simultaneously. In addition, all 39 EMBL microsatellites were assigned to individual barley chromosomes by PCR screening of wheat barley addition lines. Both studies verified a random distribution of the microsatellites within the barley genome. Subsequently, 22 EMBL microsatellites were used to assess the genetic similarity among a set of 28, mainly German, barley cultivars and two wild form accessions. Spring and winter cultivars could be easily differentiated using the first coordinate of a principal coordinate analysis. Whereas the group of spring barley cultivars appeared rather homogeneous, winter barley cultivars could be divided into three subgroups. Two H. v. ssp. spontaneum accessions were included in the assessment of genetic similarity. They were placed among the winter barley cultivars. Based on the assessment of the 30 barley cultivars and accessions, the polymorphism information content (PIC) of each EMBL microsatellite has been calculated. The average PIC value among the EMBL microsatellites was equal to 0.38, which ascertains the value of these microsatellites as a genetic tool in barley genome research projects. Received: 6 December 1999 / Accepted: 23 February 2000     

EMBLSCAN: fast approximate DNA database searches on compact disc

An algorithm that allows rapid searching of nucleic acid sequencesbased on pregenerated index files is described. The programsand index files for searching the entire EMBL nucleotide sequencecollection are being distributed on the EMBL Data Library^'sCD–ROM.     

A new HLA-B44 subtype,B*4406, differing in exon 2

The name B ^*4406 was officially assigned by the WHO Nomenclature Committee in February 1995. This follows the agreed policy that, subject to the conditions stated in the most recent Nomenclature Report (Bodmer et al. 1994), names will be assigned to new sequences as they are identified. Lists of such new names will be published in the following WHO Nomenclature Report. The nucleotide sequences reported in this Papers have been submitted to the EMBL nucleotide sequence database and have been assigned the accession numbers X83400 (HLA-B promoter region), X83401 (exon 1), X83402 (exon 2), and X83403 (exon 3)     

A newHLA-DRB1 * 13 allele (DRB1 * 1318) with a shortDRB1*08 sequence

The nucleotide sequence data reported in this paper have been submitted to the EMBL/GenBank nucleotide sequence database and have been assigned the accession number Z48631. The name listed for this sequence was officially assigned by the WHO Nomenclature Committee in November 1994. This follows the agreed policy that, subject to the conditions stated in the most recent Nomenclature Report (Bodmer et al. 1994), names will be assigned to new sequences as they are identified. Lists of such new names will be published in the following WHO Nomenclature Report     

New services of the EMBL Data Library.

The existing services of the EMBL Data Library for external users have been improved and extended in several ways. The EMBL File Server has been reorganised, and many new databases and other information relevant to biologists are now accessible via global computer networks. A broad range of software for molecular biology is freely available for different popular computer systems, including the EMBL enhancements to the Wisconsin (GCG) Package. The new Mail-Quicksearch and Mail-FastA services give access to the latest sequence data for database searches by ordinary electronic mail.     

Meeting Report: EMBL Conference - Omics and Personalized Medicine: February 16-18, 2012, Heidelberg, Germany

The first EMBL conference on "Omics and Personalized Medicine", jointly organized by Rudi Balling (LCSB, Luxembourg), Leroy Hood, Wolfgang Huber (EMBL, Heidelberg, Germany) and Lars Steinmetz (EMBL) addresses the potential and challenges of translating systems biology research into the clinic. This meeting report provides a highlight of the conference, covering not only the science, but also social and legal issues.     

园艺植物分子育种相关生物信息资源及其应用

园艺植物分子育种中,生物信息技术是一项新技术.GenBank、EMBL、DDBJ、Swiss-Prot等数据库及其序列查询系统、序列比对软件和序列提交软件是园艺植物分子育种中的重要生物信息资源.本文综述了这些生物信息资源,以及它们在克隆新基因、预测新序列功能、鉴定种质资源和进行系谱分析等方面的应用.     

园艺植物分子育种相关生物信息资源及其应用

园艺植物分子育种中, 生物信息技术是一项新技术。GenBank、EMBL、DDBJ、Swiss-Prot等数据库及其序列查询系统、序列比对软件和序列提交软件是园艺植物分子育种中的重要生物信息资源。本文综述了这些生物信息资源, 以及它们在克隆新基因、预测新序列功能、鉴定种质资源和进行系谱分析等方面的应用。     

Rapid Method for Identification of Interconnections between Functionally and/or Evolutionarily Related Biological Sequences

It is now common practice to retrieve, by key words, highly specialized selections of sequences from general-purpose databases such as EMBL, GenBank, etc. The sequences included in a selection are often interconnected, which means that there are duplications, embeddings, intersections, homology, common structural elements. Knowledge of these interconnections is necessary for further processing of the sequences. We propose a rapid (single scan) method for identification of such interconnections by means of complexity analysis that generalizes the Lempel–Ziv approach. Analysis of a selection of 5"-flanking regions of vertebrate growth hormone genes from EMBL is presented as an example.     

Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more

Genome Information Broker (GIB) is a powerful tool for the study of comparative genomics. GIB allows users to retrieve and display partial and/or whole genome sequences together with the relevant biological annotation. GIB has accumulated all the completed microbial genome and has recently been expanded to include Arabidopsis thaliana genome data from DDBJ/EMBL/GenBank. In the near future, hundreds of genome sequences will be determined. In order to handle such huge data, we have enhanced the GIB architecture by using XML, CORBA and distributed RDBs. We introduce the new GIB here. GIB is freely accessible at http://gib.genes.nig.ac.jp/.     

Living on the edge

A report on the Second EMBL/EMBO Symposium on Functional Genomics: 'Exploring the Edges of Omics', European Molecular Biology Laboratory (EMBL), Heidelberg, Germany, 16-19 October 2004.     

From metaphor to practices: The introduction of "information engineers" into the first DNA sequence database

This paper explores the introduction of professional systems engineers and information management practices into the first centralized DNA sequence database, developed at the European Molecular Biology Laboratory (EMBL) during the 1980s. In so doing, it complements the literature on the emergence of an information discourse after World War II and its subsequent influence in biological research. By the careers of the database creators and the computer algorithms they designed, analyzing, from the mid-1960s onwards information in biology gradually shifted from a pervasive metaphor to be embodied in practices and professionals such as those incorporated at the EMBL. I then investigate the reception of these database professionals by the EMBL biological staff, which evolved from initial disregard to necessary collaboration as the relationship between DNA, genes, and proteins turned out to be more complex than expected. The trajectories of the database professionals at the EMBL suggest that the initial subject matter of the historiography of genomics should be the long-standing practices that emerged after World War II and to a large extent originated outside biomedicine and academia. Only after addressing these practices, historians may turn to their further disciplinary assemblage in fields such as bioinformatics or biotechnology.     

Two new species of Capnobotryella from historical monuments

In this paper, two new species of Capnobotryella, melanized fungi with meristematic development, are described. On the basis of small subunit and internal transcribed sequence regions of ribosomal DNA sequencing, both of the new species are accommodated in the genus Capnobotryella: C. erdogani and C. kiziroglui. The type cultures of the taxa are in the ACBR culture collection (MA 4625, EMBL Accession Number: AJ972857.1; MA 4899, EMBL Accession Number: AJ972859.1).     

Bioinformatics Goes to School—New Avenues for Teaching Contemporary Biology

Since 2010, the European Molecular Biology Laboratory''s (EMBL) Heidelberg laboratory and the European Bioinformatics Institute (EMBL-EBI) have jointly run bioinformatics training courses developed specifically for secondary school science teachers within Europe and EMBL member states. These courses focus on introducing bioinformatics, databases, and data-intensive biology, allowing participants to explore resources and providing classroom-ready materials to support them in sharing this new knowledge with their students.In this article, we chart our progress made in creating and running three bioinformatics training courses, including how the course resources are received by participants and how these, and bioinformatics in general, are subsequently used in the classroom. We assess the strengths and challenges of our approach, and share what we have learned through our interactions with European science teachers.