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Links tagged with 'europe'

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BoxShadeTool Content

http://www.ch.embnet.org/software/BOX_form.html [open in a new window]

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DNA > DNA and Genomic Analysis
Protein > Identification, Presentation and Format
Sequence Comparison > Alignment Editing and Visualization

Printing and shading of multiple alignment files.

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links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
Swiss EMBnet node web server20037
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tagseurope protein databases protein sequence analysis sequence alignment

EBI patent sequence databaseDatabase Content

http://www.ebi.ac.uk/patentdata/nr/ [open in a new window]

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DNA > Databases

The EBI Patent Sequence Database is a collection of non-redundant patent sequence databases, which cover the EMBL-Bank nucleotides patent class and the patent protein databases and contain value-added annotations from patent documents.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
Non-redundant patent sequence databases with value-added annotations at two levels20103
NAR Database Issue 2010
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tagsalgorithms animals biotechnology computational biology europe factual databases gene expression profiling genetic databases humans patents as topic protein databases
setsEuropean Bioinformatics Institute (EBI)

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/ [open in a new window]

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Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching and Classification

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

links directory index: 250
TitlePublication YearGoogle Scholar Citation Count
Web services at the European Bioinformatics Institute-2009200935
Web services at the European bioinformatics institute2007143
SOAP-based services provided by the European Bioinformatics Institute200554
Public web-based services from the European Bioinformatics Institute200418
NAR Web Server Issue 2005NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

GXADatabase Content

http://www.ebi.ac.uk/gxa [open in a new window]

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Expression > Databases

The Gene Expression Atlas is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive of Functional Genomics Data. A simple interface allows the user to query for differential gene expression either (i) by gene names or attributes such as Gene Ontology terms, or (ii) by biological conditions, e.g. diseases, organism parts or cell types.

links directory index: 67
TitlePublication YearGoogle Scholar Citation Count
Gene expression atlas at the European bioinformatics institute201067
NAR Database Issue 2010
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tagsanimals computational biology europe gene expression profiling genetic databases humans nucleic acid databases statistical models

PDBeDatabase Content

http://wwpdb.org [open in a new window]

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Protein > Databases

The Protein Data Bank in Europe (PDBe) manages the international archive of biomacromolecular structure data as one of the partners in the Worldwide Protein Data Bank. PDBe has developed a browser to access and analyze the structural archive using classification systems. The PDBe web pages that describe individual PDB entries have plain-English summary pages and iconic representations of the contents of an entry (PDBprints). In addition, the information available for structures determined by means of NMR spectroscopy has been expanded. The SIFTS initiative provides extensive mapping data between proteins whose structures are available from the PDB and a host of other biomedical databases.

links directory index: 133
TitlePublication YearGoogle Scholar Citation Count
PDBe: Protein Data Bank in Europe201243
PDBe: Protein Data Bank in Europe201190
NAR Database Issue 2011
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tagsbiomolecular nuclear magnetic resonance europe protein conformation protein databases protein sequence analysis proteins

PDBe (formerly MSD)Database Content

http://www.ebi.ac.uk/pdbe/ [open in a new window]

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Protein > Databases

The Protein Data Bank in Europe (PDBe) is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. The database infrastructure is based on the remediated PDB archive data and a specially designed database for storing information on interactions between proteins and bound molecules. The newly designed 'PDBeView Atlas pages' provide an overview of an individual PDB entry in a user-friendly layout and serves as a starting point to further explore the information available in the PDBe database. PDBe's active involvement with the X-ray crystallography, Nuclear Magnetic Resonance spectroscopy and cryo-Electron Microscopy communities have resulted in improved tools for structure deposition and analysis.

links directory index: 51
TitlePublication YearGoogle Scholar Citation Count
PDBe: Protein Data Bank in Europe201051
NAR Database Issue 2010
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tagsamino acid sequence amino acid sequence homology animals binding sites computational biology europe genetic databases humans ligands molecular sequence data protein databases tertiary protein structure

Short Read ArchivesDatabase Content

http://www.ncbi.nlm.nih.gov/Traces/trace.cgi [open in a new window]

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DNA > Databases

The Sequence Read Archive (SRA) database provides the scientific community with an archival destination for next generation data sets. Partners of the International Nucleotide Sequencing Database Collaboration, include the National Center for Biotechnology Information (NCBI), the European Bioinformatics Institute (EBI), and the DNA Data Bank of Japan (DDBJ) have all established the SRA. Users of these resources can obtain data sets deposited in any of the three SRA instances.

links directory index: 38
TitlePublication YearGoogle Scholar Citation Count
Archiving next generation sequencing data201038
NAR Database Issue 2010
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tagsanimals computational biology dna sequence analysis europe genetic databases genomics humans japan national library of medicine (u.s.) nucleic acid databases united states

Swiss EMBnetTool Content

http://www.ch.embnet.org/ [open in a new window]

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Education > Directories and Portals

Swiss EMBnet is a web portal with links and access to various bioinformatics tools and links to institutes that are involved in bioinformatics.

This content is being maintained by lfalquet.

links directory index: 7
TitlePublication YearGoogle Scholar Citation Count
Swiss EMBnet node web server20037
NAR Web Server Issue 2003
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tagseurope protein databases protein sequence analysis sequence alignment

Universal Protein Resource (UniProt)Database Content

http://www.uniprot.org [open in a new window]

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Protein > Databases

Universal Protein Resource (UniProt) maintains a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database.

links directory index: 1408
TitlePublication YearGoogle Scholar Citation Count
Reorganizing the protein space at the Universal Protein Resource (UniProt)201213
Ongoing and future developments at the Universal Protein Resource2011154
The Universal Protein Resource (UniProt) in 2010201053
The Universal Protein Resource (UniProt)20071170
Update on genome completion and annotations: Protein Information Resource200418
NAR Database Issue 2010NAR Database Issue 2011
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tagsalgorithms amino acid sequence animals computational biology europe fungal genome human genome humans nucleic acid databases protein databases protein isoforms protein sequence analysis proteins proteome proteomics systems integration viral genome

Virtual Library of BiologyDatabase Content

http://www.vifabio.de/?lang=en [open in a new window]

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Education > Directories and Portals
Education > General

The Virtual Library of Biology (vifabio) offers a central entry-point for searching literature and biological subject information in libraries and on the Internet. With a single query in the Virtual Catalogue, the subject catalogues of many large libraries, major article databases (such as PubMeb), the Biodiversity Heritage Library and vifabio’s Internet Guide are searched in parallel. Links to the electronic journals library and delivery services simplify access to full-text.

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tagsbibliographic databases controlled vocabulary europe information services publications publishing pubmed

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