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

Tarkowska, 2018, Eleven quick tips to build a usable REST API for life sciences, PLoS Comput. Biol., 14, e1006542, 10.1371/journal.pcbi.1006542

Camacho, 2009, BLAST+: architecture and applications, BMC Bioinformatics, 10, 421, 10.1186/1471-2105-10-421

Pearson, 1988, Improved tools for biological sequence comparison, Proc. Natl. Acad. Sci. U.S.A., 85, 2444, 10.1073/pnas.85.8.2444

Potter, 2018, HMMER web server: 2018 update, Nucleic Acids Res., 46, W200, 10.1093/nar/gky448

Jones, 2014, InterProScan 5: Genome-scale protein function classification, Bioinformatics, 30, 1236, 10.1093/bioinformatics/btu031

Chojnacki, 2017, Programmatic access to bioinformatics tools from EMBL-EBI update: 2017, Nucleic Acids Res., 45, W550, 10.1093/nar/gkx273

Park, 2017, The EBI search engine: EBI search as a service - Making biological data accessible for all, Nucleic Acids Res., 45, W545, 10.1093/nar/gkx359

Bateman, 2018, UniProt: a worldwide hub of protein knowledge, Nucleic Acids Res., 47, D506

Silvester, 2018, The European Nucleotide Archive in 2017, Nucleic Acids Res., 46, D36, 10.1093/nar/gkx1125

Kersey, 2018, Ensembl Genomes 2018: An integrated omics infrastructure for non-vertebrate species, Nucleic Acids Res., 46, D802, 10.1093/nar/gkx1011

Burley, 2018, Protein Data Bank: the single global archive for 3D macromolecular structure data, Nucleic Acids Res., 47, D520

Mitchell, 2018, InterPro in 2019: improving coverage, classification and access to protein sequence annotations, Nucleic Acids Res., 47, D351, 10.1093/nar/gky1100

Dana, 2018, SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins, Nucleic Acids Res., 47, 482, 10.1093/nar/gky1114

Sweeney, 2018, RNAcentral: a hub of information for non-coding RNA sequences, Nucleic Acids Res., 47, D221

Perez-Riverol, 2017, Discovering and linking public omics data sets using the Omics Discovery Index, Nat. Biotechnol., 35, 406, 10.1038/nbt.3790

Amstutz, 2016, Common Workflow Language, v1.0

Rice, 2000, EMBOSS: The European molecular biology open software suite, Trends Genet., 16, 276, 10.1016/S0168-9525(00)02024-2

Waterhouse, 2009, Jalview Version 2—a multiple sequence alignment editor and analysis workbench, Bioinformatics, 25, 1189, 10.1093/bioinformatics/btp033

Ettwiller, 2005, The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates, Genome Biol., 6, R104, 10.1186/gb-2005-6-12-r104

Jareborg, 1999, Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs, Genome Res., 9, 815, 10.1101/gr.9.9.815

de Castro, 2006, ScanProsite: Detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins, Nucleic Acids Res., 34, W362, 10.1093/nar/gkl124

Katoh, 2013, MAFFT multiple sequence alignment software version 7: Improvements in performance and usability, Mol. Biol. Evol., 30, 772, 10.1093/molbev/mst010

Berger, 2011, Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood, Syst. Biol., 60, 291, 10.1093/sysbio/syr010

Rawlings, 2018, The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database, Nucleic Acids Res., 46, D624, 10.1093/nar/gkx1134

Gaulton, 2017, The ChEMBL database in 2017, Nucleic Acids Res., 45, D945, 10.1093/nar/gkw1074

Robinson, 2015, The IPD and IMGT/HLA database: allele variant databases, Nucleic Acids Res., 43, D423, 10.1093/nar/gku1161

Gou, 2015, Europe PMC: A full-text literature database for the life sciences and platform for innovation, Nucleic Acids Res., 43, D1042, 10.1093/nar/gku1061

Faulconbridge, 2014, Updates to BioSamples database at European Bioinformatics Institute, Nucleic Acids Res., 42, D50, 10.1093/nar/gkt1081

Kalvari, 2018, Rfam 13.0: Shifting to a genome-centric resource for non-coding RNA families, Nucleic Acids Res., 46, D335, 10.1093/nar/gkx1038

Jupp, 2015, A new Ontology Lookup Service at EMBL-EBI

Tryka, 2014, NCBI’s database of genotypes and phenotypes: DbGaP, Nucleic Acids Res., 42, D975, 10.1093/nar/gkt1211

Cook, 2016, The European Bioinformatics Institute in 2016: data growth and integration, Nucleic Acids Res., 44, D20, 10.1093/nar/gkv1352

Ison, 2016, Tools and data services registry: a community effort to document bioinformatics resources, Nucleic Acids Res., 44, D38, 10.1093/nar/gkv1116

McDowall, 2015, PomBase 2015: updates to the fission yeast database, Nucleic Acids Res., 43, D656, 10.1093/nar/gku1040