Web Services at the European Bioinformatics Institute

We present a new version of the European Bioinformatics Institute Web Services, a complete suite of SOAP-based web tools for structural and functional analysis, with new and improved applications. New functionality has been added to most of the services already available, and an improved version of the underlying framework has allowed us to include more applications. Information on the EBI Web Services, tutorials and clients can be found at http://www.ebi.ac.uk/Tools/webservices.

• Publication year

  2007

• Venue

  Nucleic Acids Res.

• Publication date

  2007-06-18

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/nar/gkm291PMID 17576686PMCID 1933145
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Recent developments in the MAFFT multiple sequence alignment program

  2008cited by this paper
• InterPro: the integrative protein signature database

  2008cited by this paper
• The Ontology Lookup Service: more data and better tools for controlled vocabulary queries

  2008cited by this paper
• Petabyte-scale innovations at the European Nucleotide Archive

  2008cited by this paper
• Clustal W and Clustal X version 2.0

  2007cited by this paper
• New developments in the InterPro database

  2007cited by this paper
• The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases

  2007cited by this paper
• The Universal Protein Resource (UniProt)

  2006cited by this paper
• Genome-wide analysis of transcriptional dependence and probable target sites for Abf1 and Rap1 in Saccharomyces cerevisiae

  2006cited by this paper
• Taverna: a tool for building and running workflows of services

  2006cited by this paper
• The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries

  2006cited by this paper
• Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor

  2006cited by this paper
• EMBL Nucleotide Sequence Database in 2006

  2006cited by this paper
• ProFunc: a server for predicting protein function from 3D structure

  2005cited by this paper
• BioMOBY Successfully Integrates Distributed Heterogeneous Bioinformatics Web Services. The PlaNet Exemplar Case1

  2005cited by this paper
• InterProScan: protein domains identifier

  2005cited by this paper
• Sequence analysis Blast 2 GO : a universal tool for annotation , visualization and analysis in functional genomics research

  2005cited by this paper
• Database resources of the National Center for Biotechnology Information

  2005cited by this paper
• MAFFT version 5: improvement in accuracy of multiple sequence alignment

  2005cited by this paper
• BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

  2005cited by this paper
• From genomics to chemical genomics: new developments in KEGG

  2005cited by this paper
• SOAP-based services provided by the European Bioinformatics Institute

  2005cited by this paper
• Minimum information requested in the annotation of biochemical models (MIRIAM)

  2005cited by this paper
• Kalign – an accurate and fast multiple sequence alignment algorithm

  2005cited by this paper
• LGICdb: a manually curated sequence database after the genomes

  2005cited by this paper
• Triana: a graphical Web service composition and execution toolkit

  2004cited by this paper
• Public web-based services from the European Bioinformatics Institute

  2004cited by this paper
• The European Bioinformatics Institute's data resources: towards systems biology

  2004cited by this paper
• The EMBL Nucleotide Sequence Database

  2004cited by this paper
• A combined transmembrane topology and signal peptide prediction method.

  2004cited by this paper
• The Jalview Java alignment editor

  2004cited by this paper
• Integr8 and Genome Reviews: integrated views of complete genomes and proteomes

  2004cited by this paper
• MUSCLE: a multiple sequence alignment method with reduced time and space complexity

  2004cited by this paper
• MUSCLE: multiple sequence alignment with high accuracy and high throughput.

  2004cited by this paper
• Expression Profiler: next generation - an online platform for analysis of microarray data

  2004cited by this paper
• NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

  2004cited by this paper
• The Universal Protein Resource (UniProt)

  2004cited by this paper
• DBJ in the stream of various biological data

  2004cited by this paper
• BIND: the Biomolecular Interaction Network Database

  2003cited by this paper
• EnsMart: a generic system for fast and flexible access to biological data.

  2003cited by this paper
• Soaplab - a unified Sesame door to analysis tools

  2003cited by this paper
• ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins

  2003cited by this paper
• A Life Scientist's Gateway to Distributed Data Management and Computing: The PathPort/ToolBus Framework

  2003cited by this paper
• T-Coffee: A novel method for fast and accurate multiple sequence alignment.

  2000cited by this paper
• Gene Ontology: tool for the unification of biology

  2000cited by this paper
• Architectural Styles and the Design of Network-based Software Architectures"; Doctoral dissertation

  2000cited by this paper
• EMBOSS: the European Molecular Biology Open Software Suite.

  2000cited by this paper
• DaliLite workbench for protein structure comparison

  2000cited by this paper
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

  1997cited by this paper
• Dali/FSSP classification of three-dimensional protein folds

  1997cited by this paper
• CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

  1994cited by this paper
• Database algorithm for generating protein backbone and side-chain co-ordinates from a C alpha trace application to model building and detection of co-ordinate errors.

  1991cited by this paper
• Basic local alignment search tool.

  1990cited by this paper
• Improved tools for biological sequence comparison.

  1988cited by this paper
• Identification of common molecular subsequences.

  1981cited by this paper
• A general method applicable to the search for similarities in the amino acid sequence of two proteins.

  1970cited by this paper
• Electronic Reprint Biological Crystallography the Protein Data Bank Biological Crystallography the Protein Data Bank

  year unknowncited by this paper
• Electronic Reprint Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions

  year unknowncited by this paper

• Bespoke strategies of Paxillus involutus to extract potassium from diverse phyllosilicates.

  2024cites this paper
• The IPD-IMGT/HLA Database

  2022cites this paper
• Structure of the catalytically active APOBEC3G bound to a DNA oligonucleotide inhibitor reveals tetrahedral geometry of the transition state

  2022cites this paper
• Deciphering Human Leukocyte Antigen Susceptibility Maps From Immunopeptidomics Characterization in Oncology and Infections

  2021cites this paper
• Bioinformatics of thymidine metabolism in Trypanosoma evansi: exploring nucleoside deoxyribosyltransferase (NDRT) as a drug target.

  2021cites this paper
• Fungal taste for minerals: the ectomycorrhizal fungus Paxillus involutus triggers specific genes when extracting potassium from different silicates

  2021cites this paper
• Crystal structure of a soluble APOBEC3G variant suggests ssDNA to bind in a channel that extends between the two domains.

  2020cites this paper
• UCSF ChimeraX: Structure visualization for researchers, educators, and developers

  2020cites this paper
• Metabolic drug targets of the cytosine metabolism pathways in the dromedary camel (Camelus dromedarius) and blood parasite Trypanosoma evansi

  2020cites this paper
• Exploring NIR Aza-BODIPY-Based Polarity Sensitive Probes with ON-and-OFF Fluorescence Switching in Pluronic Nanoparticles

  2020cites this paper
• Characterization of gene promoters in pig: conservative elements, regulatory motifs and evolutionary trend

  2019cites this paper
• Immunoinformatics: In Silico Approaches and Computational Design of a Multi-epitope, Immunogenic Protein

  2019cites this paper
• An Adapter Architecture for Heterogeneous Data Processing in Bioinformatics Pipelines

  2019cites this paper
• Occurrence of Acanthamoeba genotypes in Central West Malaysian environments.

  2018cites this paper
• Patterns and effects of GC3 heterogeneity and parsimony informative sites on the phylogenetic tree of genes.

  2018cites this paper
• Extending Web Services Architecture with Agent Models and Patterns

  2018cites this paper
• ExtendAlign: a computational algorithm for delivering multiple, local end-to-end alignments

  2018cites this paper
• Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA

  2018cites this paper
• Using Metadata for Locating Genomic Datasets on a Global Scale

  2018cites this paper
• The transcriptional landscape of Rhizoctonia solani AG1-IA during infection of soybean as defined by RNA-seq

  2017cites this paper
• Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas

  2017cites this paper
• Superior Multiplexing Capacity of PlexPrimers Enables Sensitive and Specific Detection of SNPs and Clustered Mutations in qPCR

  2017cites this paper
• Cryptic gene pools in the Hypericum perforatum–H. maculatum complex: diploid persistence versus trapped polyploid melting

  2017cites this paper
• Dynamic changes of tumor gene expression during repeated pressurized intraperitoneal aerosol chemotherapy (PIPAC) in women with peritoneal cancer

  2016cites this paper
• Expression profiling and characterization of cold, freezing-related genes from Brassica rapa cultivars

  2016cites this paper
• The IPD-IMGT/HLA Database - New developments in reporting HLA variation.

  2016cites this paper
• Identification and Assessment of the Potential Allergenicity of 7S Vicilins in Olive (Olea europaea L.) Seeds

  2016cites this paper
• A comparative study on the regulatory region of the PERIOD1 gene among diurnal/nocturnal primates

  2016cites this paper
• Modeling of the hEP1 receptor based on the crystallographic structure of β2-adrenergic receptor and its assessment with docking studies and molecular dynamics simulation

  2015cites this paper
• The development of computational methods for large-scale comparisons and analyses of genome evolution

  2015cites this paper
• On the Use of XMDD in Software Development Education

  2015cites this paper
• Efforts towards accessible and reliable bioinformatics

  2015cites this paper
• Distribution of HIV-1 subtypes circulating in Slovakia (2009-2012).

  2014influential citation
• ANTIMYCOBACTERIAL AND CYTOTOXICITY EVALUATION OF THE CONSTITUENTS OF MONODORA CAROLINAE

  2014cites this paper
• Data Mining for Unidentified Protein Sequences

  2014cites this paper
• Title Identification of iron transporters expressed in the magnetotactic bacteriummagnetospirillum magnetotacticum

  2014cites this paper
• Sex- and tissue-specific profiles of chemosensory gene expression in a herbivorous gall-inducing fly (Diptera: Cecidomyiidae)

  2014cites this paper
• Convertibilité entre types d'entrée et de sortie pour la composition de services en bio-informatique

  2014cites this paper
• Generating Data Converters to Help Compose Services in Bioinformatics Workflows

  2014cites this paper
• BBProF: An Asynchronous Application Server for Rapid Identification of Proteins Associated with Bacterial Bioleaching

  2014cites this paper
• The Course's SIB Libraries

  2014cites this paper
• Diagnostic value of B‐RAFV600E in difficult‐to‐diagnose thyroid nodules using fine‐needle aspiration: Systematic review and meta‐analysis

  2014cites this paper
• Modeling and Execution of Scientific Workflows with the jABC Framework

  2014cites this paper
• Constructing a Phylogenetic Tree

  2014cites this paper
• A practical approach to reconstruct evolutionary history of animal sialyltransferases and gain insights into the sequence-function relationships of Golgi-glycosyltransferases.

  2013cites this paper
• MAPI: a software framework for distributed biomedical applications

  2013cites this paper
• Functional Analysis of Novel Polymorphisms in the Human SLCO1A2 Gene that Encodes the Transporter OATP1A2

  2013cites this paper
• Human Language Technologies : The 2013 Annual Conference of the North American Chapter of the Association for Computational Linguistics Demonstration Session

  2013cites this paper
• A Fast Template Based Heuristic For Global Multiple Sequence Alignment

  2013cites this paper
• Transcriptome generation and analysis from spleen of Indian catfish, Clarias batrachus (Linnaeus, 1758) through normalized cDNA library

  2013cites this paper
• Gene ontology based characterization of expressed sequence tags (ESTs) of Brassica rapa cv. Osome.

  2013cites this paper
• Acanthamoeba genotype T4 detected in naturally-infected feline corneas found to be in homology with those causing human keratitis.

  2013cites this paper
• A Web Application for the Diagnostic Evaluation of Machine Translation over Specific Linguistic Phenomena

  2013cites this paper
• Gene Prioritization of Resistant Rice Gene against Xanthomas oryzae pv. oryzae by Using Text Mining Technologies

  2013cites this paper
• Deploying and sharing U-Compare workflows as web services

  2013cites this paper
• Expression of hsp70, hsp100 and ubiquitin in Aloe barbadensis Miller under direct heat stress and under temperature acclimation conditions

  2013cites this paper
• Synthetic Biology Approaches to Engineering Human Cells

  2013cites this paper
• Bioinformatics Approach to understand and Exploit the Potential of Lipases

  2013cites this paper
• Cloud Computing for Biomedical Information Management

  2013cites this paper
• Omics Data Exploration: Across Scales and Dimensions.

  2013cites this paper
• Use of SciDBMaker as Tool for the Design of Specialized Biological Databases

  2013cites this paper
• Antennal transcriptome analysis of the chemosensory gene families in the tree killing bark beetles, Ips typographus and Dendroctonus ponderosae (Coleoptera: Curculionidae: Scolytinae)

  2013cites this paper
• Antimicrobial Peptides: Their History, Evolution, and Functional Promiscuity

  2013cites this paper
• Evolution of lanthipeptide synthetases

  2012cites this paper
• D471G Mutation in LCMV-NP Affects its Ability to Self-associate and Results in a Dominant Negative Effect in Viral RNA Synthesis

  2012cites this paper
• SUB1A-dependent and -independent mechanisms are involved in the flooding tolerance of wild rice species.

  2012cites this paper
• Molecular phylogeny of extant equids and effects of ancestral polymorphism in resolving species-level phylogenies.

  2012cites this paper
• Targeting essential cell wall lipase Rv3802c for potential therapeutics against tuberculosis.

  2012cites this paper
• GPEC: A Cytoscape plug-in for random walk-based gene prioritization and biomedical evidence collection

  2012cites this paper
• Dermacentor variabilis: characterization and modeling of macrophage migration inhibitory factor with phylogenetic comparisons to other ticks, insects and parasitic nematodes.

  2012cites this paper
• Intelligent health information system to empower patients with chronic diseases

  2012cites this paper
• Bioinformatics Web Services

  2012cites this paper
• Generation, functional analysis and utility of Citrus grandis EST from a flower-derived cDNA library

  2012cites this paper
• Bioinformatic Tools for the Search of Disease-Associated Variations

  2012cites this paper
• Determinants for Activation of the Atypical AGC Kinase Greatwall during M Phase Entry

  2012cites this paper
• Phylogeny, Hybridization, and Evolution of Habit and Breeding System in Sidalcea and Eremalche (Malvaceae)

  2012cites this paper
• Evaluating fossil calibrations for dating phylogenies in light of rates of molecular evolution: a comparison of three approaches.

  2012cites this paper
• Web tools for predictive toxicology model building

  2012cites this paper
• Comparative Transcriptome Analysis of Two Olive Cultivars in Response to NaCl-Stress

  2012cites this paper
• MotViz: A Tool for Sequence Motif Prediction in Parallel to Structural Visualization and Analyses

  2012cites this paper
• Arnica (Asteraceae) phylogeny revisited using RPB2: complex patterns and multiple d-paralogues.

  2012cites this paper
• Scientific Workflows: Eternal Components, Changing Interfaces, Varying Compositions

  2012cites this paper
• Homology modeling of the structure of acyl coA:isopenicillin N-acyltransferase (IAT) from Penicillium chrysogenum. IAT interaction studies with isopenicillin-N, combining molecular dynamics simulations and docking

  2012cites this paper
• A tunable zinc finger-based framework for Boolean logic computation in mammalian cells

  2012cites this paper
• Exploring the factors determining the dynamics of different protein folds

  2011cites this paper
• Unraveling new genes associated with seed development and metabolism in Bixa orellana L. by expressed sequence tag (EST) analysis

  2011cites this paper
• Generation, Annotation and Analysis of First Large-Scale Expressed Sequence Tags from Developing Fiber of Gossypium barbadense L

  2011cites this paper
• Complement factor H dysfunction in atypical hemolytic uremic syndrome

  2011cites this paper
• In silico gene expression analysis in Codonopsis lanceolata root

  2011cites this paper
• Integrative network alignment reveals large regions of global network similarity in yeast and human

  2011cites this paper
• OrchidBase: a collection of sequences of the transcriptome derived from orchids.

  2011cites this paper
• Gene discovery in Triatoma infestans

  2011cites this paper
• Sequence context for transcription and translation of the Arabidopsis RPL23aA and RPL23aB paralogs.

  2011cites this paper
• Molecular targets of phytochemicals for cancer prevention

  2011cites this paper
• GeneReporter—sequence-based document retrieval and annotation

  2011cites this paper
• Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus

  2011cites this paper
• Biogen Base-An Interactive Maize Database for Phenomics Platform

  2011cites this paper
• In silico prediction of transcriptional factor-binding sites.

  2011cites this paper
• Visual Analytics and Interactive Technologies: Data, Text and Web Mining Applications

  2011cites this paper
• Sequence context for transcription and translation of the Arabidopsis RPL23aA and RPL23aB paralogs.

  2011cites this paper