Abstract
AbstractThe European Bioinformatics Institute (EMBL‐EBI)’s Job Dispatcher framework provides access to a wide range of core databases and analysis tools that are of key importance in bioinformatics. As well as providing web interfaces to these resources, web services are available using REST and SOAP protocols that enable programmatic access and allow their integration into other applications and analytical workflows and pipelines. This article describes the various options available to researchers and bioinformaticians who would like to use our resources via the web interface employing RESTful web services clients provided in Perl, Python, and Java or who would like to use Docker containers to integrate the resources into analysis pipelines and workflows. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Retrieving data from EMBL‐EBI using Dbfetch via the web interfaceAlternate Protocol 1: Retrieving data from EMBL‐EBI using WSDbfetch via the REST interfaceAlternate Protocol 2: Retrieving data from EMBL‐EBI using Dbfetch via RESTful web services with Python clientSupport Protocol 1: Installing Python REST web services clientsBasic Protocol 2: Sequence similarity search using FASTA search via the web interfaceAlternate Protocol 3: Sequence similarity search using FASTA via RESTful web services with Perl clientSupport Protocol 2: Installing Perl REST web services clientsBasic Protocol 3: Sequence similarity search using NCBI BLAST+ RESTful web services with Python clientBasic Protocol 4: Sequence similarity search using HMMER3 phmmer REST web services with Perl client and DockerSupport Protocol 3: Installing Docker and running the EMBL‐EBI client containerBasic Protocol 5: Protein functional analysis using InterProScan 5 RESTful web services with the Python client and DockerAlternate Protocol 4: Protein functional analysis using InterProScan 5 RESTful web services with the Java clientSupport Protocol 4: Installing Java web services clientsBasic Protocol 6: Multiple sequence alignment using Clustal Omega via web interfaceAlternate Protocol 5: Multiple sequence alignment using Clustal Omega with Perl client and DockerSupport Protocol 5: Exploring the RESTful API with OpenAPI User Inferface
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