The EMBL-EBI search and sequence analysis tools APIs in 2019

By Fábio Madeira, Young M. Park, Joon Lee, Nicola Buso, Tamer Gur, Nandana Madhusoodanan, Prasad Basutkar, Adrian R. N. Tivey, Simon C. Potter, Robert D. Finn and 1 more. 2019

3,783 citations recorded by the source corpus.

Abstract The EMBL-EBI provides free access to popular bioinformatics sequence analysis applications as well as to a full-featured text search engine with powerful cross-referencing and data retrieval capabilities. Access to these services is provided via user-friendly web interfaces and via established RESTful and SOAP Web Services APIs (https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBL-EBI+Web+Services+APIs+-+Data+Retrieval). Both systems have been developed with the same core principles that allow them to integrate an ever-increasing volume of biological data, making them an integral part of many popular data resources provided at the EMBL-EBI. Here, we describe the latest improvements made to the frameworks which enhance the interconnectivity between public EMBL-EBI resources and ultimately enhance biological data discoverability, accessibility, interoperability and reusability.

Subfields: Ecology, Molecular Biology

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Citations in the corpus

Sampling alternative conformational states of transporters and receptors with AlphaFold2 (2022, methodology): “…templates were used: OF MCT1 with FucB (PDB 3O7Pa and 3O7Qa, 18% sequence identity calculated using Needleman Wunsch Needleman and Wunsch, 1970 ; Madeira et al., 2019 ); OF LAT1 with AdiC (3OB6a and 5J4Ib, 22%); IF LAT1 with b(0,+)AT1 (6LI9, 45%), KCC3 (6Y5Ra, 12%), GkApcT (6F34a, 24%), NKCC1…”
Protein Sequence Analysis Using the MPI Bioinformatics Toolkit (2020, background): “…O’Donovan, & The UniProt Consortium, 2016; The UniProt Consortium, 2019)]; and integrative Web resources [the EMBL-EBI Bioin-formatics Web Services (Madeira et al., 2019; Madeira, Madhusoodanan, Lee, Tivey, & Lopez, 2019), the SIB Bioinformatics Resource Portal (Swiss Institute of Bioinformatics…”
Performance and its limits in rigid body protein-protein docking (2020, positive): “(2) Each chain is aligned to a set of known heavy and light chains using CLUSTAL (Madeira et al., 2019) and scored according to the alignment.”
Search and sequence analysis tools services from EMBL-EBI in 2022 (2022, neutral): “Trends in tool usage and citation data of our most recent article describing the framework (4) since 2019 highlight how core bioinformatics applications for sequence searching and alignment are fundamental for life sciences research and development, ranging from structural biology and drug…”
The IPD-IMGT/HLA Database (2022, methodology): “• Sequence Search Tools – Integration into the suite of search tools provided by the EMBL-EBI include EB-eye (46), FASTA and BLAST (47,48) search tools.”
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022 (2021, methodology): “And BIG Search, a distributed and scalable search engine, has been updated by including standardized data indexes from all resources in CNCB-NGDC, 39 partner resources (see details at https://ngdc.cncb.ac.cn/partners) as well as European Bioinformatics Institute (EBI) resources based on EBI Search R”
Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein (2020, positive): “Primary sequence alignment of ORF8 homologs was performed using the ClustalOmega server (26).”
IPD-IMGT/HLA Database (2019, methodology): “This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. have been incorporated i”