A new bioinformatics analysis tools framework at EMBL–EBI

By Mickael Goujon, Hamish McWilliam, Weizhong Li, F. Valentin, Silvano Squizzato, J. Pärn, Rodrigo Lopez. Nucleic Acids Res., 2010

1,942 citations recorded by the source corpus.

The EMBL-EBI provides access to various mainstream sequence analysis applications. These include sequence similarity search services such as BLAST, FASTA, InterProScan and multiple sequence alignment tools such as ClustalW, T-Coffee and MUSCLE. Through the sequence similarity search services, the users can search mainstream sequence databases such as EMBL-Bank and UniProt, and more than 2000 completed genomes and proteomes. We present here 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. These services are available over the web and via Web Services interfaces for users who require systematic access or want to interface with customized pipe-lines and workflows using common programming languages. The framework features novel result visualizations and integration of domain and functional predictions for protein database searches. It is available at http://www.ebi.ac.uk/Tools/sss for sequence similarity searches and at http://www.ebi.ac.uk/Tools/msa for multiple sequence alignments.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/80e86c8ca16da71d7ff279619d7b72c82a14f564

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

In Spectroscopy

Citations in the corpus

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA (2012, background): “For a complete picture on the enzyme properties BRENDA includes data from many external sources such as genome sequences [EBI Genomes Server (10), Ensembl database (11)], protein sequences [UniProt databases (12,13)], functional assignments [COG database (14)], molecular pathways [KEGG database (15)”
IPD—the Immuno Polymorphism Database (2012, neutral): “These tools are either custom written for the database or are incorporated into existing tools on the European Bioinformatics Institute (EBI) website, see Figure 1 (1,2).”
Analysis Tool Web Services from the EMBL-EBI (2013, methodology): “Most of the analysis tool services are implemented using a job dispatcher framework, JDispatcher (16), which provides a web interface and SOAP & REST Web Services interfaces.”
The IMGT/HLA database (2008, methodology): “Some of these tools were custom written for the IMGT/HLA database, and others were incorporated from the existing set of tools provided on the European Bioinformatics Institute’s (EBI) website (35,36).”
Reorganizing the protein space at the Universal Protein Resource (UniProt) (2011, methodology): “Sequence similarity search results which have been adapted to the new EMBL-EBI framework for web services tools (9) can be filtered by taxonomy to gain a quick overview of the taxonomic distribution of the results.”
The IPD and IMGT/HLA database: allele variant databases (2014, methodology): “Some of these tools were custom written for the IMGT/HLA Database, whereas others were incorporated from the existing set of tools described on the EBI website (18,19).”
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”
InterPro in 2011: new developments in the family and domain prediction database (2011, background): “uk/Tools/pfa/iprscan/); (ii) programmatically via Web services (19) that allow up to 25 sequences to be analysed per request (SOAP-based service documented at http://www.”
Immune epitope database analysis resource (2012, methodology): “The output page (Figure 2) provides mapping of the epitope to the source sequence, the PDB hits that contain the epitope regions, secondary structures and solvent accessibilities for each residue, presented in the format of either pairwise or multiple sequence alignment for the selected PDB hits, ob”
The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud (2013, background): “Large bioinformatics services providers, such as the EBI and the NCBI, routinely offer Web Service access to their resources in either REST or WSDL format (2).”