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Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
TLDR
A new program called Clustal Omega is described, which can align virtually any number of protein sequences quickly and that delivers accurate alignments, and which outperforms other packages in terms of execution time and quality. Expand
InterProScan 5: genome-scale protein function classification
TLDR
A new Java-based architecture for the widely used protein function prediction software package InterProScan is described, resulting in a flexible and stable system that is able to use both multiprocessor machines and/or conventional clusters to achieve scalable distributed data analysis. Expand
A new bioinformatics analysis tools framework at EMBL–EBI
TLDR
A new framework aimed at both novice as well as expert users that exposes novel methods of obtaining annotations and visualizing sequence analysis results through one uniform and consistent interface is presented. Expand
Analysis Tool Web Services from the EMBL-EBI
TLDR
Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces, which allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. Expand
The EMBL-EBI bioinformatics web and programmatic tools framework
TLDR
The EMBL-EBI Job Dispatcher framework has provided free access to a range of mainstream sequence analysis applications, and new tools and updates such as NCBI BLAST+, InterProScan 5 and PfamScan, ensure that the framework remains relevant to today's biological community. Expand
UniProt: the universal protein knowledgebase
  • Alex Maria Jesus Claire Michele Emanuele Ricardo Benoit Bateman Martin O’Donovan Magrane Alpi Antunes Bely, A. Bateman, +124 authors J. Zhang
  • Nucleic Acids Research
  • 28 November 2016
Abstract The UniProt knowledgebase is a large resource of protein sequences and associated detailed annotation. The database contains over 60 million sequences, of which over half a million sequencesExpand
Web services at the European Bioinformatics Institute-2009
TLDR
The European Bioinformatics Institute (EMBL-EBI) has been providing access to mainstream databases and tools in bioInformatics since 1997, and APIs exist for core data resources such as EMBL-Bank, Ensembl, UniProt, InterPro, PDB and ArrayExpress that allow users to systematically access databases and analytical tools. Expand
Content discovery and retrieval services at the European Nucleotide Archive
TLDR
A brief update on ENA content and some major developments undertaken in data submission services during 2014 are given and the services ENA offers for data discovery and retrieval are described. Expand
Assembly information services in the European Nucleotide Archive
TLDR
The European Nucleotide Archive content and growth over 2013 is reviewed, rapidly developing services for genome assembly information are described and further major developments over the last year are outlined. Expand
PSI-Search: iterative HOE-reduced profile SSEARCH searching
Summary: Iterative similarity searches with PSI-BLAST position-specific score matrices (PSSMs) find many more homologs than single searches, but PSSMs can be contaminated when homologous alignmentsExpand
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