Analysis Tool Web Services from the EMBL-EBI
By Hamish McWilliam, Weizhong Li, Mahmut Uludag, Silvano Squizzato, Young M. Park, Nicola Buso, Andrew Peter Cowley, Rodrigo Lopez. Nucleic Acids Res., 2013
1,684 citations recorded by the source corpus.
Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services (http://www.ebi.ac.uk/Tools/webservices/) interfaces to these databases and tools allow their integration into other tools, applications, web sites, pipeline processes and analytical workflows. To get users started using the Web Services, sample clients are provided covering a range of programming languages and popular Web Service tool kits, and a brief guide to Web Services technologies, including a set of tutorials, is available for those wishing to learn more and develop their own clients. Users of the Web Services are informed of improvements and updates via a range of methods.
Subfields: Molecular Biology, Spectroscopy
View Paper: https://www.semanticscholar.org/paper/4014007a2135ed33885d59ecf3b05162ad8537dc
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In Molecular Biology
- Rodrigo Lopez
- Young M. Park
- Fábio Madeira
- Adrian R. N. Tivey
- Joon Lee
- Nandana Madhusoodanan
- Casey S. Greene
- Deborah A. Hogan
In Spectroscopy
Citations in the corpus
- ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions (2016, methodology): “Orthologous genes across 13 strains were aligned using Clustal Omega (65) via the EMBL-EBI webserver (66), and the alignment results, including percent identity matrices and phylogenetic trees, were downloaded.”
- The EMBL-EBI bioinformatics web and programmatic tools framework (2015, methodology): “In 2009 the Job Dispatcher framework (2,3) was released to provide consistent, robust and updatable access to modern bioinformatics tools such as NCBI BLAST+ (4) and PSI-Search (5) for sequence similarity searching; InterProScan (6) and PfamScan (7) for protein functional analysis; and multiple sequ”
- Using EMBL‐EBI Services via Web Interface and Programmatically via Web Services (2014, methodology): “Since 1995, the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools using web services technologies (Chojnacki, Cowley, Lee, Foix, & Lopez, 2017; Li et al., 2015; Madeira et al., 2019; McWilliam et al., 2013).”
- CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides (2015, methodology): “Multiple sequence alignments of each AMP family were created us-ing Clustal Omega (16,17) and these were used as input to build HMM models using ‘hmmbuild’ program of HM-MER 3.1b1 package (18).”