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1.
A new service provided by EMBL (EMBL Softsvare File Server)is described that will make free molecular biology softwareavailable to anyone with computer network access. MSDOS,Apple Macintosh and VAX/VMX are supported at the moment. Theprograms will be delivered by normal electronic mail; conversionmechanisms will transfor binary files to ASCII to allow mailtransfer. This service will also help authors to distributetheir software conveniently. 相似文献
2.
GENEUS, a computer system for DNA and protein sequence analysis containing an information retrieval system for the EMBL data library. 总被引:26,自引:3,他引:23
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We describe a comprehensive computer system, GENEUS, for extensive DNA, RNA and protein sequence analysis. The analysis system is developed for the DEC VAX/VMS computer and uses the EMBL Nucleic Acid Sequence Data Library. Help information is available on-line on terminal screen. To speed up system handling, a qualifier oriented user communication is employed. All results are stored on files making them accessible to the computer editor. An information retrieval system for the EMBL Nucleotide Sequence Data Library is also described. A defined data-base interface allows connection to other analysis programs.+ 相似文献
3.
Trans-splicing of pre-mRNA is predicted to occur in a wide range of organisms including vertebrates. 总被引:2,自引:0,他引:2
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Several known trans-splicing RNA structures were used to define a canonical trans-splicing structure which was then used to perform a computer search of the EMBL nucleotide database. In addition to most known trans-splicing structures, many putative new trans-splicing sites were detected. These were found in a broad range of organisms including the vertebrates. Control experiments indicate that the search predicts known false positives at a rate of only 20%. Trans-splicing may therefore be a very wide-spread phenomenon. 相似文献
4.
5.
EBI databases and services 总被引:2,自引:0,他引:2
Rodriguez-Tomé P 《Molecular biotechnology》2001,18(3):199-212
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.
For more information, visit the EBI Web server at http://www.ebi.ac.uk/. 相似文献
6.
Stoesser G Baker W van den Broek A Camon E Garcia-Pastor M Kanz C Kulikova T Lombard V Lopez R Parkinson H Redaschi N Sterk P Stoehr P Tuli MA 《Nucleic acids research》2001,29(1):17-21
The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank at the NCBI (USA). Data is exchanged amongst the collaborating databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via ftp, email and World Wide Web interfaces. EBI's Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many specialized databases. For sequence similarity searching a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. 相似文献
7.
Mattaj I 《Current biology : CB》2005,15(3):R75-R77
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. 相似文献
8.
García-Sancho M 《History and philosophy of the life sciences》2011,33(1):71-104
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. 相似文献
9.
Mapping new EMBL-derived barley microsatellites and their use in differentiating German barley cultivars 总被引:12,自引:4,他引:8
K. Pillen A. Binder B. Kreuzkam L. Ramsay R. Waugh J. Förster J. Léon 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,101(4):652-660
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 相似文献
10.
Baker W van den Broek A Camon E Hingamp P Sterk P Stoesser G Tuli MA 《Nucleic acids research》2000,28(1):19-23
The European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database (http://www.ebi.ac. uk/embl/index.html ) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank (USA). Data is exchanged amongst the collaborative databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups. WEBIN is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via Internet and WWW interfaces. EBI's Sequence Retrieval System (SRS) is a network browser for databanks in molecular biology, integrating and linking the main nucleotide and protein databases plus many specialised databases. For sequence similarity searching a variety of tools (e.g., BLITZ, FASTA, BLAST) are available which allow external users to compare their own sequences against the most currently available data in the EMBL Nucleotide Sequence Database and SWISS-PROT. 相似文献
11.
The EMBL Data Library was the first internationally supported central resource for nucleic acid sequence data. Working in close collaboration with its American counterpart, GenBank (1), the library prepares and makes available to the scientific community a comprehensive collection of the published nucleic acid sequences. This paper describes briefly the contents of the database, how it is available, and possible future enhancements of Data Library services. 相似文献
12.
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 相似文献
13.
EMBL-Search: a CD-ROM based database query system 总被引:1,自引:0,他引:1
This paper describes a system of generally applicable indexfiles provided on the EMBL sequence databases CDROM tofacilitate the development offronzend software to thesequence databases available on this CDROM. The indexfiles are used by a new versatile and userfriendly databaseretrieval program for the Apple Macintosh, EMBLSearch,which allows the easy construction of complex database queries.EMBLSearch utilizes crossreference informationcontained in the databases to support navigation between differentinformation resources. The ability to run EMBLSearchon a local computer network accessing a shared database CDROMmakes its use particularly cost effective. 相似文献
14.
This paper describes the databases and services of the European Bioinformatics Institute (EBI). In collaboration with DDBJ and GenBank/NCBI, the EBI maintains and distributes the EMBL Nucleotide Sequence Database, Europe's primary nucleotide sequence data resource. The EBI also maintains and distributes the SWISS-PROT Protein Sequence Database, in collaboration with Amos Bairoch of the University of Geneva. Over thirty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists, are also available. The EBI network services include database searching, entry retrieval, and sequence similarity searching facilities. 相似文献
15.
The European Bioinformatics Institute (EBI) maintains and distributes the EMBL Nucleotide Sequence database, Europe's primary nucleotide sequence data resource. The EBI also maintains and distributes the SWISS-PROT Protein Sequence database, in collaboration with Amos Bairoch of the University of Geneva. Over fifty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists are available. The EBI network services include database searching and sequence similarity searching facilities. 相似文献
16.
Leinonen R Nardone F Oyewole O Redaschi N Stoehr P 《Bioinformatics (Oxford, England)》2003,19(14):1861-1862
SUMMARY: The EMBL Nucleotide Sequence Database, maintained at the European Bioinformatics institute, is Europe's primary nucleotide sequences database. Its entries are subject to changes, but only the most recent versions are preserved in the database. The EMBL Sequence Version Archive is a new publicly available database retaining also the earlier versions of these entries. AVAILABILITY: http://www.ebi.ac.uk/embl/sva/ 相似文献
17.
Guenter Stoesser Wendy Baker Alexandra van den Broek Evelyn Camon Maria Garcia-Pastor Carola Kanz Tamara Kulikova Rasko Leinonen Quan Lin Vincent Lombard Rodrigo Lopez Nicole Redaschi Peter Stoehr Mary Ann Tuli Katerina Tzouvara Robert Vaughan 《Nucleic acids research》2002,30(1):21-26
The EMBL Nucleotide Sequence Database (aka EMBL-Bank; http://www.ebi.ac.uk/embl/) incorporates, organises and distributes nucleotide sequences from all available public sources. EMBL-Bank is located and maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK. In an international collaboration with DDBJ (Japan) and GenBank (USA), data are exchanged amongst the collaborating databases on a daily basis. Major contributors to the EMBL database are individual scientists and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via FTP, email and World Wide Web interfaces. EBI’s Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many other specialized databases. For sequence similarity searching, a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. All resources can be accessed via the EBI home page at http://www.ebi.ac.uk. 相似文献
18.
MOTIVATION: While database activities in the biological area are increasing rapidly, rather little is done in the area of parsing them in a simple and object-oriented way. RESULTS: We present here an elegant, simple yet powerful way of parsing biological flat-file databases. We have taken EMBL, SWISSPROT and GENBANK as examples. EMBL and SWISS-PROT do not differ much in the format structure. GENBANK has a very different format structure than EMBL and SWISS-PROT. Extracting the desired fields in an entry (for example a sub-sequence with an associated feature) for later analysis is a constant need in the biological sequence-analysis community: this is illustrated with tools to make new splice-site databases. The interface to the parser is abstract in the sense that the access to all the databases is independent from their different formats, since parsing instructions are hidden. 相似文献
19.
The use of databanks in genetic research assumes reliability of the information they contain. Currently, error-detection in the manually or electronically entered data contained in the nucleotide sequence databanks at EMBL, Heidelberg and GenBank at Los Alamos is limited. We have used a subset of sequences from these databanks to train neural networks to recognize pre-mRNA splicing signals in human genes. During the training on 33 human genes from the EMBL databank seven genes appeared to disturb the learning process. Subsequent investigation revealed discrepancies from the original published papers, for three genes. In four genes, we found wrongly assigned splicing frames of introns. We believe this to be a reflection of the fact that splicing frames cannot always be unambiguously assigned on the basis of experimental data. Thus incorrect assignment appear both due to mere typographical misprints as well as erroneous interpretation of experiments. Training on 241 human sequences from GenBank revealed nine new errors. We propose that such errors could be detected by computer algorithms designed to check the consistency of data prior to their incorporation in databanks. 相似文献
20.
Carlos Vilches Rosario de Pablo María J. Herrero María E. Moreno Miguel Kreisler 《Immunogenetics》1994,40(4):313-313
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 相似文献