Treffer: Using EMBL-EBI Services via Web Interface and Programmatically via Web Services.
Title:
Using EMBL-EBI Services via Web Interface and Programmatically via Web Services.
Authors:
Madeira F; European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom., Madhusoodanan N; European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom., Lee J; European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom., Eusebi A; European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom., Niewielska A; European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom., Tivey ARN; European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom., Meacham S; European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom., Lopez R; European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom., Butcher S; European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
Source:
Current protocols [Curr Protoc] 2024 Jun; Vol. 4 (6), pp. e1065.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: John Wiley & Sons Country of Publication: United States NLM ID: 101773894 Publication Model: Print Cited Medium: Internet ISSN: 2691-1299 (Electronic) Linking ISSN: 26911299 NLM ISO Abbreviation: Curr Protoc Subsets: MEDLINE
Imprint Name(s):
Original Publication: Hoboken, NJ : John Wiley & Sons, [2021]-
MeSH Terms:
References:
Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI‐BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25(17), 3389–3402. https://doi.org/10.1093/nar/25.17.3389.
Bairoch, A., Boeckmann, B., Ferro, S., & Gasteiger, E. (2004). Swiss‐Prot: Juggling between evolution and stability. Briefings in Bioinformatics, 5, 39–55. https://doi.org/10.1093/bib/5.1.39.
Benson, D. A., Cavanaugh, M., Clark, K., Karsch‐Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2017). GenBank. Nucleic Acids Research, 45, D37–D42. https://doi.org/10.1093/nar/gkw1070.
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: Architecture and applications. BMC Bioinformatics, 10, 421. https://doi.org/10.1186/1471‐2105‐10‐421.
Cherry, J. M., Hong, E. L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hitz, B. C., Karra, K., Krieger, C. J., Miyasato, S. R., Nash, R. S., Park, J., Skrzypek, M. S., … Wong, E. D. (2012). Saccharomyces genome database: The genomics resource of budding yeast. Nucleic Acids Research, 40, D&00–D705. https://doi.org/10.1093/nar/gkr1029.
Chojnacki, S., Cowley, A., Lee, J., Foix, A., & Lopez, R. (2017). Programmatic access to bioinformatics tools from EMBL‐EBI update: 2017. Nucleic Acids Research, 45, W550–W553. https://doi.org/10.1093/nar/gkx273.
Davis, P., Zarowiecki, M., Arnaboldi, V., Becerra, A., Cain, S., Chan, J., Chen, W. J., Cho, J., da Veiga Beltrame, E., Diamantakis, S., Gao, S., Grigoriadis, D., Grove, C. A., Harris, T. W., Kishore, R., Le, T., Lee, R. Y. N., Luypaert, M., Müller, H. M., … Sternberg, P. W. (2022). WormBase in 2022‐data, processes, and tools for analyzing Caenorhabditis elegans. Genetics, 220(4), iyac003. https://doi.org/10.1093/genetics/iyac003.
Eddy, S. R. (1998). Profile hidden Markov models. Bioinformatics, 14, 755–763. https://doi.org/10.1093/bioinformatics/14.9.755.
Edman, P., Högfeldt, E., Sillén, L. G., & Kinell, P.‐O. (1950). Method for determination of the amino acid sequence in peptides. Acta Chemica Scandinavica, 4, 283–293. https://doi.org/10.3891/acta.chem.scand.04‐0283.
Franklin, R. E. (1956). Structure of tobacco mosaic virus: Location of the ribonucleic acid in the tobacco mosaic virus particle. Nature, 177, 928–930. https://doi.org/10.1038/177928b0.
Gramates, L. S., Marygold, S. J., Santos, G. D., Urbano, J. M., Antonazzo, G., Matthews, B. B., Rey, A. J., Tabone, C. J., Crosby, M. A., Emmert, D. B., Falls, K., Goodman, J. L., Hu, Y., Ponting, L., Schroeder, A. J., Strelets, V. B., Thurmond, J., Zhou, P., & the FlyBase Consortium. (2017). FlyBase at 25: Looking to the future. Nucleic Acids Research, 45, D663–D671. https://doi.org/10.1093/nar/gkw1016.
Hernandez, P., Müller, M., & Appel, R. D. (2006). Automated protein identification by tandem mass spectrometry: Issues and strategies. Mass Spectrometry Reviews, 25, 235–254. https://doi.org/10.1002/mas.20068.
Jones, P., Binns, D., Chang, H. Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., Pesseat, S., Quinn, A. F., Sangrador‐Vegas, A., Scheremetjew, M., Yong, S. Y., Lopez, R., & Hunter, S. (2014). InterProScan 5: Genome‐scale protein function classification. Bioinformatics, 30, 1236–1240. https://doi.org/10.1093/bioinformatics/btu031.
Kersey, P. J., Allen, J. E., Allot, A., Barba, M., Boddu, S., Bolt, B. J., Carvalho‐Silva, D., Christensen, M., Davis, P., Grabmueller, C., Kumar, N., Liu, Z., Maurel, T., Moore, B., McDowall, M. D., Maheswari, U., Naamati, G., Newman, V., Ong, C. K., … Yates, A. (2018). Ensembl Genomes 2018: An integrated omics infrastructure for non‐vertebrate species. Nucleic Acids Research, 46, D802–D808. https://doi.org/10.1093/nar/gkx1011.
Kodama, Y., Mashima, J., Kosuge, T., Kaminuma, E., Ogasawara, O., Okubo, K., Nakamura, Y., & Takagi, T. (2018). DNA data bank of Japan: 30th anniversary. Nucleic Acids Research, 46, D30–D35. https://doi.org/10.1093/nar/gkx926.
Ladunga, I. (2002). Finding homologs to nucleotide sequences using network BLAST searches. Current Protocols in Bioinformatics, 00, 3.3.1–3.3.25. https://doi.org/10.1002/0471250953.bi0303s00.
Larkin, A., Marygold, S. J., Antonazzo, G., Attrill, H., Dos Santos, G., Garapati, P. V., Goodman, J. L., Gramates, L. S., Millburn, G., Strelets, V. B., Tabone, C. J., Thurmond, J., & FlyBase Consortium (2020). FlyBase: Updates to the Drosophila melanogaster knowledge base. Nucleic Acids Research, 49, D899–D907. https://doi.org/10.1093/nar/gkaa1026.
Lee, R. Y. N., Howe, K. L., Harris, T. W., Arnaboldi, V., Cain, S., Chan, J., Chen, W. J., Davis, P., Gao, S., Grove, C., Kishore, R., Muller, H. M., Nakamura, C., Nuin, P., Paulini, M., Raciti, D., Rodgers, F., Russell, M., Schindelman, G., … Sternberg, P. W. (2018). WormBase 2017: Molting into a new stage. Nucleic Acids Research, 46, D869–D874. https://doi.org/10.1093/nar/gkx998.
Li, W., Cowley, A., Uludag, M., Gur, T., McWilliam, H., Squizzato, S., Park, Y. M., Buso, N., & Lopez, R. (2015). The EMBL‐EBI bioinformatics web and programmatic tools framework. Nucleic Acids Research, 43, W580–W584. https://doi.org/10.1093/nar/gkv279.
Lopez, R., Duggan, K., Harte, N., & Kibria, A. (2003). Public services from the European Bioinformatics Institute. Briefings in Bioinformatics, 4, 332–340. https://doi.org/10.1093/bib/4.4.332.
Madeira, F., Madhusoodanan, N., Lee, J., Eusebi, A., Niewielska, A., Tivey, A. R. N., Lopez, R., & Butcher, S. (2024). The EMBL‐EBI Job Dispatcher sequence analysis tools framework in 2024. Nucleic Acids Research, gkae241. https://doi.org/10.1093/nar/gkac241.
Madeira, F., Park, Y. M., Lee, J., Buso, N., Gur, T., Madhusoodanan, N., Basutkar, P., Tivey, A. R. N., Potter, S. C., Finn, R. D., & Lopez, R. (2019). The EMBL‐EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Research, 47, W597–600. https://doi.org/10.1093/nar/gkz268.
Madeira, F., Pearce, M., Tivey, A. R. N., Basutkar, P., Lee, J., Edbali, O., Madhusoodanan, N., Kolesnikov, A., & Lopez, R. (2022). Search and sequence analysis tools services from EMBL‐EBI in 2022. Nucleic Acids Research, 50, W276–W279. https://doi.org/10.1093/nar/gkac240.
Martin, F. J., Amode, M. R., Aneja, A., Austine‐Orimoloye, O., Azov, A. G., Barnes, I., Becker, A., Bennett, R., Berry, A., Bhai, J., Bhurji, S. K., Bignell, A., Boddu, S., Branco Lins, P. R., Brooks, L., Ramaraju, S. B., Charkhchi, M., Cockburn, A., Da Rin Fiorretto, L., … Flicek, P. (2023). Ensembl 2023. Nucleic Acids Research, 51, D933–D941. https://doi.org/10.1093/nar/gkac958.
McWilliam, H., Li, W., Uludag, M., Squizzato, S., Park, Y. M., Buso, N., Cowley, A. P., & Lopez, R. (2013). Analysis tool web services from the EMBL‐EBI. Nucleic Acids Research, 41, W597–600. https://doi.org/10.1093/nar/gkt376.
McWilliam, H., Valentin, F., Goujon, M., Li, W., Narayanasamy, M., Martin, J., Miyar, T., & Lopez, R. (2009). Web services at the European Bioinformatics Institute‐2009. Nucleic Acids Research, 37, W6–W10. https://doi.org/10.1093/nar/gkp302.
Mulder, N. J., & Apweiler, R. (2003). The InterPro database and tools for protein domain analysis. Current Protocols in Bioinformatics, 2, 2.7.1–2.7.19. https://doi.org/10.1002/0471250953.bi0207s02.
Park, Y. M., Squizzato, S., Buso, N., Gur, T., & Lopez, R. (2017). The EBI search engine: EBI search as a service—Making biological data accessible for all. Nucleic Acids Research, 45, W545–W549. https://doi.org/10.1093/nar/gkx359.
Pearson, W. R. (2016). Finding protein and nucleotide similarities with FASTA. Current Protocols in Bioinformatics, 53, 3.9.1–3.9.25. https://doi.org/10.1002/0471250953.bi0309s53.
Pearson, W. R., & Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences, 85, 2444–2448. https://doi.org/10.1073/pnas.85.8.2444.
Pettersson, E., Lundeberg, J., & Ahmadian, A. (2009). Generations of sequencing technologies. Genomics, 93, 105–111. https://doi.org/10.1016/j.ygeno.2008.10.003.
Potter, S. C., Luciani, A., Eddy, S. R., Park, Y., Lopez, R., & Finn, R. D. (2018). HMMER web server: 2018 update. Nucleic Acids Research, 46, W200–W204. https://doi.org/10.1093/nar/gky448.
Roberts, R. J., & Murray, K. (1976). Restriction endonuclease. Critical Reviews in Biochemistry and Molecular Biology, 4, 123–164. https://doi.org/10.3109/10409237609105456.
Sanger, F., & Coulson, A. R. (1975). A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. Journal of Molecular Biology, 94, 441k–448. https://doi.org/10.1016/0022‐2836(75)90213‐2.
Sayers, E. W., Cavanaugh, M., Clark, K., Pruitt, K. D., Sherry, S. T., Yankie, L., & Karsch‐Mizrachi, I. (2024). GenBank 2024 update. Nucleic Acids Research, 52(D1), D134–D137. https://doi.org/10.1093/nar/gkad903.
Schwartz, E. M., & Sternberg, P. W. (2004). Searching WormBase for information about Caenorhabditis elegans. Current Protocols in Bioinformatics, 6, 1.8.1–1.8.44. https://doi.org/10.1002/0471250953.bi0108s6.
Shank, S. D., Weaver, S., & Pond, S. L. K. (2018). phylotree.js—A JavaScript library for application development and interactive data visualization in phylogenetics. BMC Bioinformatics, 19, 276. https://doi.org/10.1186/s12859‐018‐2283‐2.
Sievers, F., & Higgins, D. G. (2014). Clustal Omega. Current Protocols in Bioinformatics, 48, 3.13.1–3.13.16. https://doi.org/10.1002/0471250953.bi0313s48.
Sievers, F., & Higgins, D. G. (2018). Clustal Omega for making accurate alignments of many protein sequences. Protein Science, 27, 135–145. https://doi.org/10.1002/pro.3290.
Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., Thompson, J. D., & Higgins, D. G. (2011). Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7, 539. https://doi.org/10.1038/msb.2011.75.
Silvester, N., Alako, B., Amid, C., Cerdeño‐Tarrága, A., Clarke, L., Cleland, I., Harrison, P. W., Jayathilaka, S., Kay, S., Keane, T., Leinonen, R., Liu, X., Martínez‐Villacorta, J., Menchi, M., Reddy, K., Pakseresht, N., Rajan, J., Rossello, M., Smirnov, D., … Cochrane, G. (2018). The European nucleotide archive in 2017. Nucleic Acids Research, 46, D36–D40. https://doi.org/10.1093/nar/gkx1125.
Skrzypek, M. S., & Hirschman, J. (2011). Using the Saccharomyces Genome Database (SGD) for analysis of genomic information. Current Protocols in Bioinformatics, 35, 1.20.1–1.20.23. https://doi.org/10.1002/0471250953.bi0120s35.
Squizzato, S., Park, Y. M., Buso, N., Gur, T., Cowley, A., Li, W., Uludag, M., Pundir, S., Cham, J. A., McWilliam, H., & Lopez, R. (2015). The EBI Search engine: Providing search and retrieval functionality for biological data from EMBL‐EBI. Nucleic Acids Research, 43, W585–W588. https://doi.org/10.1093/nar/gkv316.
Tanizawa, Y., Fujisawa, T., Kodama, Y., Kosuge, T., Mashima, J., Tanjo, T., & Nakamura, Y. (2023). DNA Data Bank of Japan (DDBJ) update report 2022. Nucleic Acids Research, 51, D101–D105. https://doi.org/10.1093/nar/gkac1083.
UniProt Consortium. (2019). UniProt: A worldwide hub of protein knowledge. Nucleic Acids Research, 47(D1), D506–D515. https://doi.org/10.1093/nar/gky1049.
UniProt Consortium. (2023). UniProt: The universal protein knowledgebase in 2023. Nucleic Acids Research, 51, D523–D531. https://doi.org/10.1093/nar/gkac1052.
Valentin, F., Squizzato, S., Goujon, M., McWilliam, H., Paern, J., & Lopez, R. (2010). Fast and efficient searching of biological data resources‐using EB‐eye. Briefings in Bioinformatics, 11, 375–384. https://doi.org/10.1093/bib/bbp065.
Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M., & Barton, G. J. (2009). Jalview version 2‐A multiple sequence alignment editor and analysis workbench. Bioinformatics, 25, 1189–1191. https://doi.org/10.1093/bioinformatics/btp033.
Wolfsberg, T. G. (2007). Using the NCBI map viewer to browse genomic sequence data. Current Protocols in Bioinformatics, 16, 1.5.1–1.5.22. https://doi.org/10.1002/0471250953.bi0105s16.
Wu, C., & Nebert, D. W. (2004). Update on genome completion and annotations: Protein information resource. Human Genomics, 1, 229–233. https://doi.org/10.1186/1479‐7364‐1‐3‐229.
Yuan, D., Ahamed, A., Burgin, J., Cummins, C., Devraj, R., Gueye, K., Gupta, D., Gupta, V., Haseeb, M., Ihsan, M., Ivanov, E., Jayathilaka, S., Kadhirvelu, V. B., Kumar, M., Lathi, A., Leinonen, R., McKinnon, J., Meszaros, L., O'Cathail, C., … Cochrane, G. (2024). The European nucleotide archive in 2023. Nucleic Acids Research, 52(D1), D92–D97. https://doi.org/10.1093/nar/gkad1067.
Zerbino, D. R., Achuthan, P., Akanni, W., Amode, M. R., Barrell, D., Bhai, J., Billis, K., Cummins, C., Gall, A., Girón, C. G., Gil, L., Gordon, L., Haggerty, L., Haskell, E., Hourlier, T., Izuogu, O. G., Janacek, S. H., Juettemann, T., To, J. K., … Flicek, P. (2018). Ensembl 2018. Nucleic Acids Research, 46, D754–D761. https://doi.org/10.1093/nar/gkx1098.
Bairoch, A., Boeckmann, B., Ferro, S., & Gasteiger, E. (2004). Swiss‐Prot: Juggling between evolution and stability. Briefings in Bioinformatics, 5, 39–55. https://doi.org/10.1093/bib/5.1.39.
Benson, D. A., Cavanaugh, M., Clark, K., Karsch‐Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2017). GenBank. Nucleic Acids Research, 45, D37–D42. https://doi.org/10.1093/nar/gkw1070.
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: Architecture and applications. BMC Bioinformatics, 10, 421. https://doi.org/10.1186/1471‐2105‐10‐421.
Cherry, J. M., Hong, E. L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S. R., Fisk, D. G., Hirschman, J. E., Hitz, B. C., Karra, K., Krieger, C. J., Miyasato, S. R., Nash, R. S., Park, J., Skrzypek, M. S., … Wong, E. D. (2012). Saccharomyces genome database: The genomics resource of budding yeast. Nucleic Acids Research, 40, D&00–D705. https://doi.org/10.1093/nar/gkr1029.
Chojnacki, S., Cowley, A., Lee, J., Foix, A., & Lopez, R. (2017). Programmatic access to bioinformatics tools from EMBL‐EBI update: 2017. Nucleic Acids Research, 45, W550–W553. https://doi.org/10.1093/nar/gkx273.
Davis, P., Zarowiecki, M., Arnaboldi, V., Becerra, A., Cain, S., Chan, J., Chen, W. J., Cho, J., da Veiga Beltrame, E., Diamantakis, S., Gao, S., Grigoriadis, D., Grove, C. A., Harris, T. W., Kishore, R., Le, T., Lee, R. Y. N., Luypaert, M., Müller, H. M., … Sternberg, P. W. (2022). WormBase in 2022‐data, processes, and tools for analyzing Caenorhabditis elegans. Genetics, 220(4), iyac003. https://doi.org/10.1093/genetics/iyac003.
Eddy, S. R. (1998). Profile hidden Markov models. Bioinformatics, 14, 755–763. https://doi.org/10.1093/bioinformatics/14.9.755.
Edman, P., Högfeldt, E., Sillén, L. G., & Kinell, P.‐O. (1950). Method for determination of the amino acid sequence in peptides. Acta Chemica Scandinavica, 4, 283–293. https://doi.org/10.3891/acta.chem.scand.04‐0283.
Franklin, R. E. (1956). Structure of tobacco mosaic virus: Location of the ribonucleic acid in the tobacco mosaic virus particle. Nature, 177, 928–930. https://doi.org/10.1038/177928b0.
Gramates, L. S., Marygold, S. J., Santos, G. D., Urbano, J. M., Antonazzo, G., Matthews, B. B., Rey, A. J., Tabone, C. J., Crosby, M. A., Emmert, D. B., Falls, K., Goodman, J. L., Hu, Y., Ponting, L., Schroeder, A. J., Strelets, V. B., Thurmond, J., Zhou, P., & the FlyBase Consortium. (2017). FlyBase at 25: Looking to the future. Nucleic Acids Research, 45, D663–D671. https://doi.org/10.1093/nar/gkw1016.
Hernandez, P., Müller, M., & Appel, R. D. (2006). Automated protein identification by tandem mass spectrometry: Issues and strategies. Mass Spectrometry Reviews, 25, 235–254. https://doi.org/10.1002/mas.20068.
Jones, P., Binns, D., Chang, H. Y., Fraser, M., Li, W., McAnulla, C., McWilliam, H., Maslen, J., Mitchell, A., Nuka, G., Pesseat, S., Quinn, A. F., Sangrador‐Vegas, A., Scheremetjew, M., Yong, S. Y., Lopez, R., & Hunter, S. (2014). InterProScan 5: Genome‐scale protein function classification. Bioinformatics, 30, 1236–1240. https://doi.org/10.1093/bioinformatics/btu031.
Kersey, P. J., Allen, J. E., Allot, A., Barba, M., Boddu, S., Bolt, B. J., Carvalho‐Silva, D., Christensen, M., Davis, P., Grabmueller, C., Kumar, N., Liu, Z., Maurel, T., Moore, B., McDowall, M. D., Maheswari, U., Naamati, G., Newman, V., Ong, C. K., … Yates, A. (2018). Ensembl Genomes 2018: An integrated omics infrastructure for non‐vertebrate species. Nucleic Acids Research, 46, D802–D808. https://doi.org/10.1093/nar/gkx1011.
Kodama, Y., Mashima, J., Kosuge, T., Kaminuma, E., Ogasawara, O., Okubo, K., Nakamura, Y., & Takagi, T. (2018). DNA data bank of Japan: 30th anniversary. Nucleic Acids Research, 46, D30–D35. https://doi.org/10.1093/nar/gkx926.
Ladunga, I. (2002). Finding homologs to nucleotide sequences using network BLAST searches. Current Protocols in Bioinformatics, 00, 3.3.1–3.3.25. https://doi.org/10.1002/0471250953.bi0303s00.
Larkin, A., Marygold, S. J., Antonazzo, G., Attrill, H., Dos Santos, G., Garapati, P. V., Goodman, J. L., Gramates, L. S., Millburn, G., Strelets, V. B., Tabone, C. J., Thurmond, J., & FlyBase Consortium (2020). FlyBase: Updates to the Drosophila melanogaster knowledge base. Nucleic Acids Research, 49, D899–D907. https://doi.org/10.1093/nar/gkaa1026.
Lee, R. Y. N., Howe, K. L., Harris, T. W., Arnaboldi, V., Cain, S., Chan, J., Chen, W. J., Davis, P., Gao, S., Grove, C., Kishore, R., Muller, H. M., Nakamura, C., Nuin, P., Paulini, M., Raciti, D., Rodgers, F., Russell, M., Schindelman, G., … Sternberg, P. W. (2018). WormBase 2017: Molting into a new stage. Nucleic Acids Research, 46, D869–D874. https://doi.org/10.1093/nar/gkx998.
Li, W., Cowley, A., Uludag, M., Gur, T., McWilliam, H., Squizzato, S., Park, Y. M., Buso, N., & Lopez, R. (2015). The EMBL‐EBI bioinformatics web and programmatic tools framework. Nucleic Acids Research, 43, W580–W584. https://doi.org/10.1093/nar/gkv279.
Lopez, R., Duggan, K., Harte, N., & Kibria, A. (2003). Public services from the European Bioinformatics Institute. Briefings in Bioinformatics, 4, 332–340. https://doi.org/10.1093/bib/4.4.332.
Madeira, F., Madhusoodanan, N., Lee, J., Eusebi, A., Niewielska, A., Tivey, A. R. N., Lopez, R., & Butcher, S. (2024). The EMBL‐EBI Job Dispatcher sequence analysis tools framework in 2024. Nucleic Acids Research, gkae241. https://doi.org/10.1093/nar/gkac241.
Madeira, F., Park, Y. M., Lee, J., Buso, N., Gur, T., Madhusoodanan, N., Basutkar, P., Tivey, A. R. N., Potter, S. C., Finn, R. D., & Lopez, R. (2019). The EMBL‐EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Research, 47, W597–600. https://doi.org/10.1093/nar/gkz268.
Madeira, F., Pearce, M., Tivey, A. R. N., Basutkar, P., Lee, J., Edbali, O., Madhusoodanan, N., Kolesnikov, A., & Lopez, R. (2022). Search and sequence analysis tools services from EMBL‐EBI in 2022. Nucleic Acids Research, 50, W276–W279. https://doi.org/10.1093/nar/gkac240.
Martin, F. J., Amode, M. R., Aneja, A., Austine‐Orimoloye, O., Azov, A. G., Barnes, I., Becker, A., Bennett, R., Berry, A., Bhai, J., Bhurji, S. K., Bignell, A., Boddu, S., Branco Lins, P. R., Brooks, L., Ramaraju, S. B., Charkhchi, M., Cockburn, A., Da Rin Fiorretto, L., … Flicek, P. (2023). Ensembl 2023. Nucleic Acids Research, 51, D933–D941. https://doi.org/10.1093/nar/gkac958.
McWilliam, H., Li, W., Uludag, M., Squizzato, S., Park, Y. M., Buso, N., Cowley, A. P., & Lopez, R. (2013). Analysis tool web services from the EMBL‐EBI. Nucleic Acids Research, 41, W597–600. https://doi.org/10.1093/nar/gkt376.
McWilliam, H., Valentin, F., Goujon, M., Li, W., Narayanasamy, M., Martin, J., Miyar, T., & Lopez, R. (2009). Web services at the European Bioinformatics Institute‐2009. Nucleic Acids Research, 37, W6–W10. https://doi.org/10.1093/nar/gkp302.
Mulder, N. J., & Apweiler, R. (2003). The InterPro database and tools for protein domain analysis. Current Protocols in Bioinformatics, 2, 2.7.1–2.7.19. https://doi.org/10.1002/0471250953.bi0207s02.
Park, Y. M., Squizzato, S., Buso, N., Gur, T., & Lopez, R. (2017). The EBI search engine: EBI search as a service—Making biological data accessible for all. Nucleic Acids Research, 45, W545–W549. https://doi.org/10.1093/nar/gkx359.
Pearson, W. R. (2016). Finding protein and nucleotide similarities with FASTA. Current Protocols in Bioinformatics, 53, 3.9.1–3.9.25. https://doi.org/10.1002/0471250953.bi0309s53.
Pearson, W. R., & Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences, 85, 2444–2448. https://doi.org/10.1073/pnas.85.8.2444.
Pettersson, E., Lundeberg, J., & Ahmadian, A. (2009). Generations of sequencing technologies. Genomics, 93, 105–111. https://doi.org/10.1016/j.ygeno.2008.10.003.
Potter, S. C., Luciani, A., Eddy, S. R., Park, Y., Lopez, R., & Finn, R. D. (2018). HMMER web server: 2018 update. Nucleic Acids Research, 46, W200–W204. https://doi.org/10.1093/nar/gky448.
Roberts, R. J., & Murray, K. (1976). Restriction endonuclease. Critical Reviews in Biochemistry and Molecular Biology, 4, 123–164. https://doi.org/10.3109/10409237609105456.
Sanger, F., & Coulson, A. R. (1975). A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. Journal of Molecular Biology, 94, 441k–448. https://doi.org/10.1016/0022‐2836(75)90213‐2.
Sayers, E. W., Cavanaugh, M., Clark, K., Pruitt, K. D., Sherry, S. T., Yankie, L., & Karsch‐Mizrachi, I. (2024). GenBank 2024 update. Nucleic Acids Research, 52(D1), D134–D137. https://doi.org/10.1093/nar/gkad903.
Schwartz, E. M., & Sternberg, P. W. (2004). Searching WormBase for information about Caenorhabditis elegans. Current Protocols in Bioinformatics, 6, 1.8.1–1.8.44. https://doi.org/10.1002/0471250953.bi0108s6.
Shank, S. D., Weaver, S., & Pond, S. L. K. (2018). phylotree.js—A JavaScript library for application development and interactive data visualization in phylogenetics. BMC Bioinformatics, 19, 276. https://doi.org/10.1186/s12859‐018‐2283‐2.
Sievers, F., & Higgins, D. G. (2014). Clustal Omega. Current Protocols in Bioinformatics, 48, 3.13.1–3.13.16. https://doi.org/10.1002/0471250953.bi0313s48.
Sievers, F., & Higgins, D. G. (2018). Clustal Omega for making accurate alignments of many protein sequences. Protein Science, 27, 135–145. https://doi.org/10.1002/pro.3290.
Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., Thompson, J. D., & Higgins, D. G. (2011). Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7, 539. https://doi.org/10.1038/msb.2011.75.
Silvester, N., Alako, B., Amid, C., Cerdeño‐Tarrága, A., Clarke, L., Cleland, I., Harrison, P. W., Jayathilaka, S., Kay, S., Keane, T., Leinonen, R., Liu, X., Martínez‐Villacorta, J., Menchi, M., Reddy, K., Pakseresht, N., Rajan, J., Rossello, M., Smirnov, D., … Cochrane, G. (2018). The European nucleotide archive in 2017. Nucleic Acids Research, 46, D36–D40. https://doi.org/10.1093/nar/gkx1125.
Skrzypek, M. S., & Hirschman, J. (2011). Using the Saccharomyces Genome Database (SGD) for analysis of genomic information. Current Protocols in Bioinformatics, 35, 1.20.1–1.20.23. https://doi.org/10.1002/0471250953.bi0120s35.
Squizzato, S., Park, Y. M., Buso, N., Gur, T., Cowley, A., Li, W., Uludag, M., Pundir, S., Cham, J. A., McWilliam, H., & Lopez, R. (2015). The EBI Search engine: Providing search and retrieval functionality for biological data from EMBL‐EBI. Nucleic Acids Research, 43, W585–W588. https://doi.org/10.1093/nar/gkv316.
Tanizawa, Y., Fujisawa, T., Kodama, Y., Kosuge, T., Mashima, J., Tanjo, T., & Nakamura, Y. (2023). DNA Data Bank of Japan (DDBJ) update report 2022. Nucleic Acids Research, 51, D101–D105. https://doi.org/10.1093/nar/gkac1083.
UniProt Consortium. (2019). UniProt: A worldwide hub of protein knowledge. Nucleic Acids Research, 47(D1), D506–D515. https://doi.org/10.1093/nar/gky1049.
UniProt Consortium. (2023). UniProt: The universal protein knowledgebase in 2023. Nucleic Acids Research, 51, D523–D531. https://doi.org/10.1093/nar/gkac1052.
Valentin, F., Squizzato, S., Goujon, M., McWilliam, H., Paern, J., & Lopez, R. (2010). Fast and efficient searching of biological data resources‐using EB‐eye. Briefings in Bioinformatics, 11, 375–384. https://doi.org/10.1093/bib/bbp065.
Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M., & Barton, G. J. (2009). Jalview version 2‐A multiple sequence alignment editor and analysis workbench. Bioinformatics, 25, 1189–1191. https://doi.org/10.1093/bioinformatics/btp033.
Wolfsberg, T. G. (2007). Using the NCBI map viewer to browse genomic sequence data. Current Protocols in Bioinformatics, 16, 1.5.1–1.5.22. https://doi.org/10.1002/0471250953.bi0105s16.
Wu, C., & Nebert, D. W. (2004). Update on genome completion and annotations: Protein information resource. Human Genomics, 1, 229–233. https://doi.org/10.1186/1479‐7364‐1‐3‐229.
Yuan, D., Ahamed, A., Burgin, J., Cummins, C., Devraj, R., Gueye, K., Gupta, D., Gupta, V., Haseeb, M., Ihsan, M., Ivanov, E., Jayathilaka, S., Kadhirvelu, V. B., Kumar, M., Lathi, A., Leinonen, R., McKinnon, J., Meszaros, L., O'Cathail, C., … Cochrane, G. (2024). The European nucleotide archive in 2023. Nucleic Acids Research, 52(D1), D92–D97. https://doi.org/10.1093/nar/gkad1067.
Zerbino, D. R., Achuthan, P., Akanni, W., Amode, M. R., Barrell, D., Bhai, J., Billis, K., Cummins, C., Gall, A., Girón, C. G., Gil, L., Gordon, L., Haggerty, L., Haskell, E., Hourlier, T., Izuogu, O. G., Janacek, S. H., Juettemann, T., To, J. K., … Flicek, P. (2018). Ensembl 2018. Nucleic Acids Research, 46, D754–D761. https://doi.org/10.1093/nar/gkx1098.
Contributed Indexing:
Keywords: REST; SOAP; bioinformatics resources; bioinformatics tools; programmatic access; web services; workflows
Entry Date(s):
Date Created: 20240610 Date Completed: 20240610 Latest Revision: 20240610
Update Code:
20250114
DOI:
10.1002/cpz1.1065
PMID:
38857087
Database:
MEDLINE
Weitere Informationen
The European Bioinformatics Institute (EMBL-EBI)'s Job Dispatcher framework provides access to a wide range of core databases and analysis tools that are of key importance in bioinformatics. As well as providing web interfaces to these resources, web services are available using REST and SOAP protocols that enable programmatic access and allow their integration into other applications and analytical workflows and pipelines. This article describes the various options available to researchers and bioinformaticians who would like to use our resources via the web interface employing RESTful web services clients provided in Perl, Python, and Java or who would like to use Docker containers to integrate the resources into analysis pipelines and workflows. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Retrieving data from EMBL-EBI using Dbfetch via the web interface Alternate Protocol 1: Retrieving data from EMBL-EBI using WSDbfetch via the REST interface Alternate Protocol 2: Retrieving data from EMBL-EBI using Dbfetch via RESTful web services with Python client Support Protocol 1: Installing Python REST web services clients Basic Protocol 2: Sequence similarity search using FASTA search via the web interface Alternate Protocol 3: Sequence similarity search using FASTA via RESTful web services with Perl client Support Protocol 2: Installing Perl REST web services clients Basic Protocol 3: Sequence similarity search using NCBI BLAST+ RESTful web services with Python client Basic Protocol 4: Sequence similarity search using HMMER3 phmmer REST web services with Perl client and Docker Support Protocol 3: Installing Docker and running the EMBL-EBI client container Basic Protocol 5: Protein functional analysis using InterProScan 5 RESTful web services with the Python client and Docker Alternate Protocol 4: Protein functional analysis using InterProScan 5 RESTful web services with the Java client Support Protocol 4: Installing Java web services clients Basic Protocol 6: Multiple sequence alignment using Clustal Omega via web interface Alternate Protocol 5: Multiple sequence alignment using Clustal Omega with Perl client and Docker Support Protocol 5: Exploring the RESTful API with OpenAPI User Inferface.
(© 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.)