Cited by 698Genomics and Phylogenetic StudiesResearch Data Management PracticesScientific Computing and Data Management

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The European Nucleotide Archive

Open access

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.·2011·Nucleic Acids Research

DOI 10.1093/nar/gkq967PMC PMC3013801

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Abstract

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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Figure 1. The complete mitochondrial genome for Ursus spelaeus (cave bear) from the Max Planck Institute for Evolutionary Anthropology submitted to EMBL-Bank in 2010.CC BY-NC · PubMed Central

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The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Velvet: Algorithms for de novo short read assembly using de Bruijn graphsPreprint
Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,587 · cited 1×
“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.”
Method
Automated generation of heuristics for biological sequence comparison
Slater, G., & Birney, E. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-31 · Cited by 2,959
The International Nucleotide Sequence Database Collaboration
Karsch‐Mizrachi, I., Nakamura, Y., & Cochrane, G. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1006 · Cited by 717
GenBank
Benson, D. A., Karsch‐Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1024 · Cited by 348
Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary
Krause, J., Unger, T., Noçon, A., Malaspinas, A., Kolokotronis, S., Stiller, M., Soibelzon, L. H., Spriggs, H. F., Dear, P. H., Briggs, A. W., et al. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-220 · Cited by 288
The International Nucleotide Sequence Database Collaboration
Cochrane, G., Karsch‐Mizrachi, I., & Nakamura, Y. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1150 · Cited by 113
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).”
Method
Improvements 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).”
Background
Fast 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×
“Data can be queried using the EB-Eye free text search functionality available in the header section of all EBI web pages (7).”
Method

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Additional file 5 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
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Additional file 13 of Investigating the impact of reference assembly choice on genomic analyses in a cattle breed
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Resilience and response of marine microbes to the future ocean and a marine heatwave — insights from a mesocosm experiment
Brüwer, J. D., Reismann, M., Wichels, A., John, U., Schmidt, J., Meunier, C. L., Fuchs, B. M., & Kirstein, I. V. (2026) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiag042 · Cited by 1
“The raw sequence data is available in the European Nucleotide Archive (Leinonen et al. 2010 ) under the accession number PRJEB89385, using the data brokerage service of the German Federation for Biological Data (Diepenbroek et al. 2014 ), in compliance with the Minimal Information about any (X)…”
Genomics: Foundations, Applications, and Big Data in Health Informatics
Giannopoulou, E. G., Zhang, C., & Lu, S. L. (2026) · Health informatics · doi:10.1007/978-3-032-16657-9_17
Evolutionary diversity of sphingolipid metabolism proteins in fungi
Płecha, M., Sokołowska, B., Barua, D., Bartczak, J., Sobczyk, M., Koperska, D., Kułakowska, A., Komosa, A., & Muszewska, A. (2026) · IMA Fungus · doi:10.3897/imafungus.17.177891
“The RNA-Seq data were downloaded in the form of fastq files from the ENA server (Leinonen et al. 2011).”
Research Process Graph: LLM-Driven Extraction and Hierarchical Organization of Research LogicPreprint
Yang, J., Itharajula, M., & Mutwil, M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.09.731113
“NCBI GEO: archive for functional genomics data sets, update.”
The Sequence and the Standard: An Account of Participatory Informational Format Exclusion (PIFE)
Sheehan, N. (2026) · Social Epistemology · doi:10.1080/02691728.2026.2682153
“The INSDC’s designation of FASTQ as the required format for the Sequence Read Archive two years later (Leinonen et al. 2011) completed this process, converting a social fact into an institutional mandate.”
Bio-informatique et analyses « omiques » : chronologie d’une nouvelle approche scientifique
Bastien, S., Gourinovitch, M., Vandenesch, F., & Moreau, K. (2026) · médecine/sciences · doi:10.1051/medsci/2026105
Ancient whole genomes reveal regional selection during adaptation to Neolithic lifestyle in Western EurasiaPreprint
Schikora-Tamarit, M. À., Carrion, P., Orozco-Arias, S., Valtueña, A. A., Ivanović, A., Scheib, C. L., Kabral, H., Gut, I. G., Tambets, K., Gut, M. O., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.07.15.738373
Microbiome-based tracking of diet shifts in ectotherms: a new approach to monitor effects of global changes on food webs?Preprint
Eterovick, P. C., Ruthsatz, K., Vieira, S., Sikorski, J., Valero, K. C. W., & Overmann, J. (2026) · Research Square · doi:10.21203/rs.3.rs-8959905/v2
Scalable regional genomic surveillance reveals previously unrecognized SARS-CoV-2 recombinant diversity and limited onward transmissionPreprint
Köhler, C., Tzvetkova, A., Pohlmann, A., Lehmann, K., Sasse, T., Balau, V., Beer, M., Kaderali, L., Goller, K. V., Hübner, N., et al. (2026) · Research Square · doi:10.21203/rs.3.rs-10510603/v1
Microbiome-based tracking of diet shifts in ectotherms to monitor effects of global changes on food webs: a systematic map with identified challenges and prospectsPreprint
Eterovick, P. C., Ruthsatz, K., Vieira, S., Sikorski, J., Valero, K. C. W., & Overmann, J. (2026) · Research Square · doi:10.21203/rs.3.rs-8959905/v3
Microbial repositories and microbial databases useful for forensic research
Behzadi, P. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-40634-8.00040-4
Global in silico analysis reveals a core gut microbiota in fall armyworm ( Spodoptera frugiperda ) shaped by geography and diet
Anand, L., & Corbin, K. R. (2026) · ISME Communications · doi:10.1093/ismeco/ycag233
“Data was curated from major sequence repositories (NCBI Sequence Read Archive [ 39], the European Nucleotide Archive [ 40], and the DNA Data Bank of Japan [ 41]) using the search terms “fall armyworm,” “ S. frugiperda ,” and “fall-army-gut”.”
Unravelling the trophic ecology of the ocean sunfish Mola mola in the western Mediterranean Sea through integrated approaches
Borrajo, O., García-Barcelona, S., Fernández‐Corredor, E., Fernández‐Álvarez, F. Á., Marta Coll, M., & Navarro, J. (2026) · Reviews in Fish Biology and Fisheries · doi:10.1007/s11160-026-10083-y
“The taxonomic assignment of each ASV was performed using a classifier from the MetaCOXI reference database (Balech et al. 2022), which is based on the European Nucleotide Archive (ENA) (Leinonen et al. 2011) and the BOLD (Ratnasingham and Hebert 2007).”
scASprofiler: profiling single-cell RNA splicing with a deep convolutional generative network
Hu, P., Song, P., Dai, B., Long, C., Li, H., Zuo, Y., & Xing, Y. (2026) · Briefings in Bioinformatics · doi:10.1093/bib/bbag497
“scRNA-seq datasets generated by the SMART-seq [ 33] and 10 × Genomics [ 34] platforms were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) [ 35] and European Nucleotide Archive (ENA) [ 36].”
Insights into the dynamics of antibiotic resistance genes in the human gut microbiome across populations
Pateriya, D., Tanwar, A., & Sharma, V. K. (2026) · Gut Pathogens · doi:10.1186/s13099-026-00860-2
“Raw reads were retrieved from the NCBI Sequence Read Archive (SRA) [16] and the ENA [17].”
Evaluating Diabetes Drug Targets for Vascular Dementia Prevention Using Drug Target Mendelian RandomisationPreprint
Packer, A. E., Austin, L., Williams, D. M., Taylor‐Bateman, V., & Anderson, E. L. (2026) · medRxiv · doi:10.64898/2026.09.22.26363326
Comparative Analysis of Inhibition Efficiency of Chimeric Antisense Oligonucleotides with Various Chemical Modifications and Their Application for Exogenous Control of Gene Expression in Escherichia coli
Georgieva, A. V., & Prof. Robert Penchovsky, D. R. N. (2026) · Antibiotics · doi:10.3390/antibiotics15100985
microSTRESSdb: A curated database for prioritizing bacteria alleviating plant abiotic stress
Nuijten, P., Bretscher, K., Cazorla, R., Raaijmakers, J. M., Guillermo, G., Ossowicki, A., & Carrión, V. J. (2026) · Microbiological Research · doi:10.1016/j.micres.2026.128762
Advancing Cancer Biomarker Discovery Through Multi‐Omics, Bioinformatics, and Artificial Intelligence: A Systematic Review
Tok, P., Achari, V. M., & Chang, S. (2026) · PROTEOMICS · doi:10.1002/pmic.70196
ALLCAPS: a scalable and accurate deep-learning method for in silico pneumococcal serotypingPreprint
Tajmirriahi, A., Mateeva, T., Russell, M., Lorenz, O., Kim, S. J., Lo, S. W., Bentley, S. D., Lees, J. A., & Horsfield, S. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.10.14.759107
“Reads for all samples were downloaded from the ENA (Leinonen et al. 2011) and assembled using Shovill v1.”
FAIRsharing record for: dictyBase
FAIRsharing Team (2018) · FAIRsharing.org · doi:10.25504/fairsharing.4shj9c
Microbiome Preterm Birth DREAM Challenge
Sirota, M. (2023) · ImmPort · doi:10.21430/m316mgbo3o
FAIRsharing record for: Disbiome
FAIRsharing Team, Lister, A., & Janssens, Y. (2018) · FAIRsharing.org · doi:10.25504/fairsharing.lfdtxb
FAIRsharing record for: International Human Epigenome Consortium Data Portal
FAIRsharing Team, & Lister, A. (2022) · FAIRsharing.org · doi:10.25504/fairsharing.6f54c5
FAIRsharing record for: Enzyme Structure Function Ontology
FAIRsharing Team (2018) · FAIRsharing.org · doi:10.25504/fairsharing.9y3gv0
FAIRsharing record for: Ontology for Biomedical Investigations
FAIRsharing Team (2015) · FAIRsharing.org · doi:10.25504/fairsharing.284e1z
Toward planetary microbial systems biology
Bork, P., Bowler, C., Tedersoo, L., Kuhn, M., Bowler, C., de Vargas, C., Arendt, D., Boss, E., Lombard, F., Vincent, F., et al. (2026) · Cell · doi:10.1016/j.cell.2026.09.019
Dissemination and visualisation of biological data
Moreno, B. G. (2014) · doi:10.5821/dissertation-2117-95484
Repositories for Sharing Human Data in Stem Cell Research
Ossorio, P. N. (2013) · Springer eBooks · doi:10.1007/978-1-4614-9062-3_5
Translation of nucleotide sequences to amino acids and their comparison with data stored in databases.
Kalaycioglu, A. T. (2013) · Kafkas Universitesi Veteriner Fakultesi Dergisi

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: Leinonen, R.
Birney, E.
Cheng, Y.
Cleland, I.
Goodgame, N.
Gibson, R.
Pakseresht, N.
Plaister, S.
Radhakrishnan, R.
Vaughan, R.
Zalunin, V.
Cochrane, G.
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
DOI: 10.1093/nar/gkq967
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: cc-by-nc
creativecommons.org/licenses/by-nc/2.5 (vor, 2214 d)
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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