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The European Nucleotide Archive
Open accessAbstract
The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe's primary nucleotide-sequence repository. The ENA consists of three main databases: the Sequence Read Archive (SRA), the Trace Archive and EMBL-Bank. The objective of ENA is to support and promote the use of nucleotide sequencing as an experimental research platform by providing data submission, archive, search and download services. In this article, we outline these services and describe major changes and improvements introduced during 2010. These include extended EMBL-Bank and SRA-data submission services, extended ENA Browser functionality, support for submitting data to the European Genome-phenome Archive (EGA) through SRA, and the launch of a new sequence similarity search service.
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“Tools such as DIGIT and Abysis source their data from the European Nucleotide Archive (ENA) [60] and the National Center for Biotechnology Information (NCBI) [61]; their sequence volumes are of the order of 105 and contain multiple artificially engineered sequences.”
From Computational approaches to therapeutic antibody design: established methods and emerging trends (2020) · cites this paper as [60]
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Cites
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“Experimental search support for a limited number of raw reads is provided through De-Bruijn servers based on Velvet (9), using the Exonerate client-server protocol and being fully integrated with our search service.”
MethodAutomated generation of heuristics for biological sequence comparison
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The International Nucleotide Sequence Database Collaboration
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The International Nucleotide Sequence Database Collaboration
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DDBJ launches a new archive database with analytical tools for next-generation sequence data
Kaminuma, E., Mashima, J., Kodama, Y., Gojobori, T., Ogasawara, O., Okubo, K., Takagi, T., & Nakamura, Y. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp847 · Cited by 99 · cited 1×
“The ENA works closely together with NCBI (1) and DDBJ (2) as partners in the International Nucleotide Sequence Database Collaboration (3).”
MethodImprovements to services at the European Nucleotide Archive
Leinonen, R., Akhtar, R. A., Birney, E., Bonfield, J., Bower, L., Corbett, M., Cheng, Y., Demiralp, F., Faruque, N., Goodgame, N., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp998 · Cited by 66 · cited 1×
“It contains a large diversity of data from patent, expressed sequence tag, whole genome shotgun and other high-throughput sequences, through genomic assemblies and richly annotated sequence fragments to whole replicons (5).”
BackgroundFast and efficient searching of biological data resources--using EB-eye
Valentin, F., Squizzato, S., Goujon, M., McWilliam, H., Paern, J., & López, R. (2010) · Briefings in Bioinformatics · doi:10.1093/bib/bbp065 · Cited by 37 · cited 1×
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“The second set is the human microbiome set SRR2155174 downloaded from ENA [21].”
BackgroundSrikakulam, S. K., Keller, S., Dabbaghie, F., Bals, R., & Kalinina, O. V. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.12.456081 · Cited by 2
“With this feature, we downloaded 4 TiB of compressed Tara Oceans dataset (study accession: PRJEB1787) from the ENA archive consisting of 249 samples containing 495 FASTQ files.”
BackgroundPaving the way for FAIR data in plant phenotyping
Papoutsoglou, E. (2021) · doi:10.18174/546089 · Cited by 2
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“Indeed, the metadata retrieval, conducted through querying the ENA Browser Data API, is consequently subject to the rules of the EBI Search engine (EBI Search Documentation).”
BackgroundMethodInfluentialA human commons cell atlas reveals cell type specificity for OAS1 isoformsPreprint
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MethodPig and quail CpG methylation datasets from short and long read sequencing technologies
Terzian, P., Vandecasteele, C., Lledo, J., Serre, R.-F., Sabban, J., Kuchly, C., Frédérique Pitel, A., Leroux, S., Demars, J., Iannuccelli, N., et al. (2025) · Scientific Data · doi:10.1038/s41597-025-04769-4 · Cited by 2
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Zhao, Z., Marotta, F., & Wu, M. (2024) · Microorganisms · doi:10.3390/microorganisms12071264 · Cited by 1
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MethodKonečný, L., & Peterková, K. (2024) · Advances in Parasitology/Advances in parasitology · doi:10.1016/bs.apar.2024.05.003 · Cited by 1
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“The FASTQ files were downloaded from ENA and NCBI-SRA, and metadata was obtained from the papers and NCBI-SRA.”
Grigoriadis, D., Tsifintaris, M., Giannakakis, A., Pavlopoulos, G. A., & Perdikopanis, N. (2025) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2025.11.004 · Cited by 1
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MFPD: A Multiple Fungal Pathogen Detection Pipeline Across Diverse Habitats
Shen, Y., Yang, X., Yu, J., Zhang, Y., Yang, T., Gao, Y., Wang, X., Jousset, A., Raza, W., Zhao, F., et al. (2026) · Advanced Science · doi:10.1002/advs.202522660 · Cited by 1
Truong, V. Q., & Ritchie, M. D. (2026) · Briefings in Bioinformatics · doi:10.1093/bib/bbag256 · Cited by 1
“…successfully united the European Molecular Biology Laboratory—European Bioinformatics Institute’s European Nucleotide Archives (EMBL-EBI ENA) [ 20, 21], National Institute of Genetics’ DNA Data Bank of Japan (NIG DDBJ) [ 22], and National Center for Biotechnology Information (NCBI GenBank) […”
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“The data is at the EMBL-EBI European Nucleotide Archive, ENA [39] (identification number ERX012425).”
MethodLiu, Z., Li, J., Nie, W., Wang, R., Li, Y., Han, L., Liu, Y., & Liu, J. (2015) · Scientia Sinica Chimica · doi:10.1360/n032015-00001 · Cited by 1
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Jaber, K. M., Hamad, N. A., & Quiam, F. (2019) · International Journal of Computational and Experimental Science and Engineering · doi:10.22399/ijcesen.508889 · Cited by 1
“An example of this large increase can be found in the DDBJ, EMBL and GenBank from 1999 to 2016, its exponentially growth is presented in Figure 2, which is adapted from [9].”
BackgroundData Science of Microbiome: Does Gender Matter
Bašić-Čičak, D., & Telalović, J. H. (2022) · Lecture notes in networks and systems · doi:10.1007/978-3-031-17697-5_49 · Cited by 1
Reference-free phylogeny from sequencing data
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“The sequences were downloaded from the ENA repository [15] and were selected to contain similar virus genomes.”
MethodSaddiqa, A., Zakir, M., Sheikh, M., Muneer, Z., Hassan, A., Ali, I. F. M., Haq, I. U., Khan, A. A., Malik, A., & Siddiqi, A. R. (2024) · Scientific Reports · doi:10.1038/s41598-024-69721-9 · Cited by 1
Mousavi-Sagharchi, S. M. A., Sheykhhasan, M., Ghorbani, A., Afrazeh, E., Poondla, N., Kalhor, N., Tanzadehpanah, H., Mahaki, H., & Manoochehri, H. (2024) · Advances in bioinformatics and biomedical engineering book series · doi:10.4018/979-8-3693-3192-7.ch002 · Cited by 2
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Detection of Bacteriophages: Sequence-Based Systems
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“The short reads containing the whole-genome sequences of these 7,845 isolates were downloaded from the European Nucleotide Archive [21] and the Sequence Read Archive [22].”
MethodMDPFP-FCNN: Multidomain Protein Function Prediction Using Fuzzy Convolutional Neural Network
(2021) · International journal of intelligent engineering and systems · doi:10.22266/ijies2021.1231.57 · Cited by 1
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Membrane Clustering of Coronavirus Variants Using Document Similarity
Lehotay–Kéry, P., & Kiss, A. (2022) · Genes · doi:10.3390/genes13111966 · Cited by 1
“Data Availability Statement: We used the NCBI reference sequences (RefSeq) [25] and The European Nucleotide Archive [26] databases to collect the genomes used in this paper.”
MethodDötsch, A., Merz, B., Louis, S., Krems, C., Herrmann, M., Dörr, C., Watzl, B., Bub, A., Straßburg, A., & Engelbert, A. K. (2023) · JMIR Research Protocols · doi:10.2196/42529 · Cited by 1
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ENA (European Nucleotide Archive)
Griffith, O. L., & Griffith, M. (2004) · Dictionary of Bioinformatics and Computational Biology · doi:10.1002/9780471650126.dob0885 · Cited by 1
Bioinformatic methods for characterization of viral pathogens in metagenomic samples
Lysholm, F. (2013) · KTH Publication Database DiVA (KTH Royal Institute of Technology) · Cited by 1
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Lim, J. J. J., Koh, J., Moo, J. R., Villanueva, E. M. F., Putri, D. A., Lim, Y. S., Seetoh, W. S., Mulupuri, S., Ng, J. W. Z., Nguyen, N. L. U., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.26.174581 · Cited by 1
“RNA-sequencing experiments for all the fungal species were streamed as fastq files from the European Nucleotide Archive (ENA) (24) by using the LSTRaP-Cloud pipeline (ref).”
MethodThe Role of Selective Breeding and Microbiome Composition in Chicken Health
Zou, T. (2018) · TSpace (University of Toronto) · Cited by 1
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“Sequence data generated in biological experiments is submitted to one of the three mirroring databases of the International Nucleotide Sequence Database Collaboration (INSDC): NCBI Sequence Read Archive (SRA) [13], EBI European Nucleotide Archive (ENA) [48] and DDBJ Sequence Read Archive (DRA) [49].”
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Peace, R. (2016) · Carleton University's Institutional Repository (MacOdrum Library, Carleton University) · doi:10.22215/etd/2016-11462 · Cited by 1
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“The Raw RNA-seq data for three datasets were retrieved from the European Nucleotide Archive (ENA) database [54].”
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Кондратов, К. А., Artamonov, A. A., Nikitin, Y. V., Velmiskina, A., Mikhailovskii, V., Mosenko, S. V., Полковникова, И. А., Asinovskaya, A. Y., Апалько, С. В., Николаевна, С. Н., et al. (2024) · Preprints.org · doi:10.20944/preprints202402.0379.v1
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“After comparing all metabolites and checking their transport in the EMBL database (https://www.embl.org) (Leinonen et al., 2011), we finalized on 139 metabolites that connect the reconstruction to the gut microbiota in the colon lumen, including SCFAs and bile acids (Table S6).”
Gourdine, J.-P. F., Pacentine, I. V., Barstad, A., Dahl, E. M., Gregory, W. T., Wolfe, A. J., Sysoeva, T. A., & Karstens, L. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.02.646827 · Cited by 1
“Sequence Read Archive (SRA) and the European Nucleotide Archive (ENA) 61,62 under the accession number PRJEB8104; See Supplemental Table 2).”
FAIRsharing record for: GenBank Nucleotide Sequence Database
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Expression Analysis and Genome Annotations with RNA Sequencing
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Data integration in biological research: an
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Big Biological Data Management
Pedersen, E., & Bongo, L. A. (2016) · Computer communications and networks · doi:10.1007/978-3-319-44881-7_13
“The pipeline input data is produced by biotechnology instruments such as nextgeneration sequencing machines, or downloaded from public repositories such as GEO [10] and ENA [22].”
MethodLibrary Services for Bioinformatics
Ram, S. (2017) · Advances in library and information science (ALIS) book series · doi:10.4018/978-1-5225-1871-6.ch002
McKie, J. H., & McKie, S. A. (2017) · Future Medicinal Chemistry · doi:10.4155/fmc-2017-0032
Profiling copy number alterations in cell-free tumour DNA using a single-referencePreprint
Robertson, A. J., Xu, Q., Song, S., Ganesamoorthy, D., Benson, D., Chen, W., Ferguson, K., Nones, K., Lakhani, S. R., Simpson, P. T., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/290171
Big Data Analysis Techniques for Visualization of Genomics in Medicinal Plants
Kumar, H., Chandramohan, V., Simon, S. M., Yadav, R. S., & Kumar, S. B. (2018) · Advances in data mining and database management book series · doi:10.4018/978-1-5225-3142-5.ch026
An Introduction to Tools, Databases, and Practical Guidelines for NGS Data Analysis
Kanterakis, A., Potamias, G., & Patrinos, G. P. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809414-3.00004-8
Appearance of synthetic vector-associated antibiotic resistance genes in next-generation sequencesPreprint
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UM ESTUDO SOBRE FLUXOS DE DADOS E BANCOS DE DADOS BIOLÓGICOS
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“O repositório é conhecido por EMBL-Bank [23].”
BackgroundBioprospecting of Trichococcus species
Strepis, N. (2019) · doi:10.18174/465966
An Empirical Study on Efficient Storage of Human Genome Data
Chaudhary, D., Kahali, B., & Simmhan, Y. L. (2019) · IEEE International Conference on High Performance Computing, Data and Analytics Workshop (HiPCW) · doi:10.1109/hipcw.2019.00030
“E.g., ENA currently contains ≈ 80 trillion sequences and 12 petabases, and its data size doubles every two years.”
MethodPredicting drug resistance in M. tuberculosis using a Long-term Recurrent Convolutional NetworkPreprint
Safari, A. H., Sedaghat, N., Zabeti, H., Forna, A., Chindelevitch, L., & Libbrecht, M. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.07.372136
“The short reads containing the whole-genome sequences of these 7845 isolates are downloaded from the European Nucleotide Archive [27] and the Sequence Read Archive [28].”
MethodA resampling strategy for studying robustness in virus detection pipelines
Kohls, M., Saremi, B., Muchsin, I., Fischer, N., Becher, P., & Jung, K. (2021) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2021.107555
SeqDown: An Efficient Sequence Retrieval Software and Comparative Sequence Retrieval Analysis
Hanif, W., Fatima, H., Qasim, M., Atif, R. M., & Javed, M. R. (2021) · Current Trends in OMICS · doi:10.32350/cto.11.03
Genetic regulation of gene expression in brain and blood
de Klein, N. (2021) · University of Groningen research database (University of Groningen / Centre for Information Technology) · doi:10.33612/diss.178049845
Parker, M. D., Hedlund, E., & Zhang, J. (2013) · Elsevier eBooks · doi:10.1016/b978-0-12-396967-5.00010-4
Verschuuren, T. D. (2021) · Utrecht University Repository (Utrecht University) · doi:10.33540/779
Splicing role of PRPF40A/B paralogs in human myeloid cells
Tan, C. W. (2021) · DR-NTU (Nanyang Technological University) · doi:10.32657/10356/155738
Silicon Era of Carbon-Based Life: Application of Genomics and Bioinformatics in Crop Stress Research
Li, M., Qi, X., Ni, M., & Lam, H. (2016) · CRC Press eBooks · doi:10.1201/9781315365084-6 · Cited by 1
Library Services for Bioinformatics
Ram, S. (2019) · IGI Global eBooks · doi:10.4018/978-1-5225-8903-7.ch050
Using genome-wide expression compendia to study microorganisms
Lee, A. J., Reiter, T. E., Doing, G., Oh, J., Hogan, D. A., & Greene, C. S. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.08.012 · Cited by 1
“[48] Leinonen R, Akhtar R, Birney E, et al.”
Background
Metadata
- Authors
- Leinonen, R., Akhtar, R., Birney, E., Bower, L., Cerdeno-Tarraga, A., Cheng, Y., Cleland, I., Faruque, N., Goodgame, N., Gibson, R., Hoad, G., Jang, M., Pakseresht, N., Plaister, S., Radhakrishnan, R., Reddy, K., Sobhany, S., Ten Hoopen, P., Vaughan, R., Zalunin, V., & Cochrane, G.
- Affiliations
- European Bioinformatics Institute (GB)
- Corresponding author
- Leinonen, R.
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-10-23
- Volume
- 39
- Issue
- Database
- Pages
- D28-D31
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC3013801
- OpenAlex
- W2120358246
- Cited by
- 690
- References
- 10
- Citations by year
- 2026: 37 · 2025: 49 · 2024: 74 · 2023: 52 · 2022: 44 · 2021: 64 · 2020: 37 · 2019: 42 · 2018: 41 · 2017: 47 · 2016: 39 · 2015: 48 · 2014: 33 · 2013: 31 · 2012: 23
- FWCI
- 10.60
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- Wellcome Trust (085532)
- European Molecular Biology Laboratory
- European Commission
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- European Nucleotide Archive, Sequence Read Archive, DNA sequence databases, sequence similarity search, European Genome-phenome Archive
- MeSH terms
- Base Sequence, Europe, Databases, Nucleic Acid, Molecular Sequence Annotation, High-Throughput Nucleotide Sequencing
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