Analysis Tool Web Services from the EMBL-EBI

Analysis Tool Web Services from the EMBL-EBI

2013 | Hamish McWilliam, Weizhong Li, Mahmut Uludag, Silvano Squizzato, Young Mi Park, Nicola Buso, Andrew Peter Cowley and Rodrigo Lopez*
The European Bioinformatics Institute (EMBL-EBI) provides a range of Web Services since 2004 to access databases and analysis tools. These services include searching across databases, retrieving entry data in various formats, and using analysis tools like sequence similarity search, multiple sequence alignment, and protein functional analysis. The REST/SOAP Web Services allow integration into other tools, applications, and workflows. Sample clients and tutorials are provided for users to start using these services. The EB-eye Web Service enables searching across multiple databases and navigating cross-references, while dbfetch and WSDbfetch retrieve entry data. Entry data are available in various formats, such as UniProtKB flat-file, FASTA, GFF, XML, and SeqXML. Analysis tool services include sequence similarity search (FASTA, NCBI BLAST), multiple sequence alignment (Clustal Omega, MUSCLE), pairwise sequence alignment, and protein functional analysis (InterProScan, Phobius). These services are implemented using a job dispatcher framework, JDispatcher, which provides web interfaces and SOAP/REST interfaces. The Web Services are used in various applications, including web interfaces, desktop applications, and workflow processes. They are also used in tools like Blast2GO, BlastStation, Bioclipse, and T-COFFEE. The EMBL-EBI continues to develop new Web Services and integrate significant data workflows. The availability of these services allows developers to integrate additional functionality without maintaining their own databases or software. The EMBL-EBI aims to meet users' needs for persistency and availability, and provides documentation, sample clients, and training courses. The volume and proportion of Web Services traffic continue to increase, with a significant number of analysis jobs processed through SOAP/REST interfaces. The EMBL-EBI also provides updates and information through various communication channels to keep users informed of service changes and availability.The European Bioinformatics Institute (EMBL-EBI) provides a range of Web Services since 2004 to access databases and analysis tools. These services include searching across databases, retrieving entry data in various formats, and using analysis tools like sequence similarity search, multiple sequence alignment, and protein functional analysis. The REST/SOAP Web Services allow integration into other tools, applications, and workflows. Sample clients and tutorials are provided for users to start using these services. The EB-eye Web Service enables searching across multiple databases and navigating cross-references, while dbfetch and WSDbfetch retrieve entry data. Entry data are available in various formats, such as UniProtKB flat-file, FASTA, GFF, XML, and SeqXML. Analysis tool services include sequence similarity search (FASTA, NCBI BLAST), multiple sequence alignment (Clustal Omega, MUSCLE), pairwise sequence alignment, and protein functional analysis (InterProScan, Phobius). These services are implemented using a job dispatcher framework, JDispatcher, which provides web interfaces and SOAP/REST interfaces. The Web Services are used in various applications, including web interfaces, desktop applications, and workflow processes. They are also used in tools like Blast2GO, BlastStation, Bioclipse, and T-COFFEE. The EMBL-EBI continues to develop new Web Services and integrate significant data workflows. The availability of these services allows developers to integrate additional functionality without maintaining their own databases or software. The EMBL-EBI aims to meet users' needs for persistency and availability, and provides documentation, sample clients, and training courses. The volume and proportion of Web Services traffic continue to increase, with a significant number of analysis jobs processed through SOAP/REST interfaces. The EMBL-EBI also provides updates and information through various communication channels to keep users informed of service changes and availability.
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