Literature DB >> 15215339

Public web-based services from the European Bioinformatics Institute.

Nicola Harte1, Ville Silventoinen, Emmanuel Quevillon, Stephen Robinson, Kimmo Kallio, Xavier Fustero, Pravin Patel, Petteri Jokinen, Rodrigo Lopez.   

Abstract

The mission of the European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory (EMBL) in Heidelberg, is to ensure that the growing body of information from molecular biology and genome research is placed in the public domain and is accessible freely to all parts of the scientific community in ways that promote scientific progress. To fulfil this mission, the EBI provides a wide variety of free, publicly available bioinformatics services. These can be divided into data submissions processing; access to query, analysis and retrieval systems and tools; ftp downloads of software and databases; training and education and user support. All of these services are available at the EBI website: http://www.ebi.ac.uk/services. This paper provides a detailed introduction to the interactive analysis systems that are available from the EBI and a brief introduction to other, related services.

Mesh:

Substances:

Year:  2004        PMID: 15215339      PMCID: PMC441543          DOI: 10.1093/nar/gkh405

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  30 in total

1.  CluSTr: a database of clusters of SWISS-PROT+TrEMBL proteins.

Authors:  E V Kriventseva; W Fleischmann; E M Zdobnov; R Apweiler
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

2.  EMBOSS: the European Molecular Biology Open Software Suite.

Authors:  P Rice; I Longden; A Bleasby
Journal:  Trends Genet       Date:  2000-06       Impact factor: 11.639

3.  The GeneQuiz web server: protein functional analysis through the Web.

Authors:  S Hoersch; C Leroy; N P Brown; M A Andrade; C Sander
Journal:  Trends Biochem Sci       Date:  2000-01       Impact factor: 13.807

4.  Flexible sequence similarity searching with the FASTA3 program package.

Authors:  W R Pearson
Journal:  Methods Mol Biol       Date:  2000

5.  GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

Authors:  J Besemer; A Lomsadze; M Borodovsky
Journal:  Nucleic Acids Res       Date:  2001-06-15       Impact factor: 16.971

6.  The Ensembl genome database project.

Authors:  T Hubbard; D Barker; E Birney; G Cameron; Y Chen; L Clark; T Cox; J Cuff; V Curwen; T Down; R Durbin; E Eyras; J Gilbert; M Hammond; L Huminiecki; A Kasprzyk; H Lehvaslaiho; P Lijnzaad; C Melsopp; E Mongin; R Pettett; M Pocock; S Potter; A Rust; E Schmidt; S Searle; G Slater; J Smith; W Spooner; A Stabenau; J Stalker; E Stupka; A Ureta-Vidal; I Vastrik; M Clamp
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

7.  IMGT gene identification and Colliers de Perles of human immunoglobulins with known 3D structures.

Authors:  Manuel Ruiz; Marie-Paule Lefranc
Journal:  Immunogenetics       Date:  2002-01-30       Impact factor: 2.846

8.  InterProScan--an integration platform for the signature-recognition methods in InterPro.

Authors:  E M Zdobnov; R Apweiler
Journal:  Bioinformatics       Date:  2001-09       Impact factor: 6.937

9.  Rapid automatic detection and alignment of repeats in protein sequences.

Authors:  A Heger; L Holm
Journal:  Proteins       Date:  2000-11-01

10.  HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources.

Authors:  D Fredman; M Siegfried; Y P Yuan; P Bork; H Lehväslaiho; A J Brookes
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

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  13 in total

1.  Prenatal stress changes the glycoprotein GPM6A gene expression and induces epigenetic changes in rat offspring brain.

Authors:  Melisa C Monteleone; Ezequiela Adrover; María Eugenia Pallarés; Marta C Antonelli; Alberto C Frasch; Marcela A Brocco
Journal:  Epigenetics       Date:  2013-08-19       Impact factor: 4.528

2.  An Integrated Approach for Microprotein Identification and Sequence Analysis.

Authors:  Omar Brito-Estrada; Keira R Hassel; Catherine A Makarewich
Journal:  J Vis Exp       Date:  2022-07-12       Impact factor: 1.424

3.  EMBL Nucleotide Sequence Database: developments in 2005.

Authors:  Guy Cochrane; Philippe Aldebert; Nicola Althorpe; Mikael Andersson; Wendy Baker; Alastair Baldwin; Kirsty Bates; Sumit Bhattacharyya; Paul Browne; Alexandra van den Broek; Matias Castro; Karyn Duggan; Ruth Eberhardt; Nadeem Faruque; John Gamble; Carola Kanz; Tamara Kulikova; Charles Lee; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Michelle McHale; Hamish McWilliam; Gaurab Mukherjee; Francesco Nardone; Maria Pilar Garcia Pastor; Siamak Sobhany; Peter Stoehr; Katerina Tzouvara; Robert Vaughan; Dan Wu; Weimin Zhu; Rolf Apweiler
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

4.  EMBL Nucleotide Sequence Database in 2006.

Authors:  Tamara Kulikova; Ruth Akhtar; Philippe Aldebert; Nicola Althorpe; Mikael Andersson; Alastair Baldwin; Kirsty Bates; Sumit Bhattacharyya; Lawrence Bower; Paul Browne; Matias Castro; Guy Cochrane; Karyn Duggan; Ruth Eberhardt; Nadeem Faruque; Gemma Hoad; Carola Kanz; Charles Lee; Rasko Leinonen; Quan Lin; Vincent Lombard; Rodrigo Lopez; Dariusz Lorenc; Hamish McWilliam; Gaurab Mukherjee; Francesco Nardone; Maria Pilar Garcia Pastor; Sheila Plaister; Siamak Sobhany; Peter Stoehr; Robert Vaughan; Dan Wu; Weimin Zhu; Rolf Apweiler
Journal:  Nucleic Acids Res       Date:  2006-12-05       Impact factor: 16.971

5.  Domain organization of long autotransporter signal sequences.

Authors:  Jan A Hiss; Gisbert Schneider
Journal:  Bioinform Biol Insights       Date:  2009-12-14

6.  SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services.

Authors:  Damian D G Gessler; Gary S Schiltz; Greg D May; Shulamit Avraham; Christopher D Town; David Grant; Rex T Nelson
Journal:  BMC Bioinformatics       Date:  2009-09-23       Impact factor: 3.169

7.  Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis.

Authors:  Roberto T Arrial; Roberto C Togawa; Marcelo de M Brigido
Journal:  BMC Bioinformatics       Date:  2009-08-04       Impact factor: 3.169

8.  IPD--the Immuno Polymorphism Database.

Authors:  James Robinson; Kavita Mistry; Hamish McWilliam; Rodrigo Lopez; Steven G E Marsh
Journal:  Nucleic Acids Res       Date:  2009-10-29       Impact factor: 16.971

9.  The IMGT/HLA database.

Authors:  James Robinson; Jason A Halliwell; Hamish McWilliam; Rodrigo Lopez; Peter Parham; Steven G E Marsh
Journal:  Nucleic Acids Res       Date:  2012-10-17       Impact factor: 16.971

10.  Web services at the European bioinformatics institute.

Authors:  Alberto Labarga; Franck Valentin; Mikael Anderson; Rodrigo Lopez
Journal:  Nucleic Acids Res       Date:  2007-06-18       Impact factor: 16.971

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