The European Nucleotide Archive in 2021

Cummins, Carla; Ahamed, Alisha; Aslam, Raheela; Burgin, Josephine; Devraj, Rajkumar; Edbali, Ossama; Gupta, Dipayan; Harrison, Peter W.; Haseeb, Muhammad; Holt, Sam; Ibrahim, Talal; Ivanov, Eugene; Jayathilaka, Suran; Kadhirvelu, Vishnukumar Balavenkataraman; Kay, Simon; Kumar, Manish; Lathi, Ankur; Leinonen, Rasko; Madeira, Fábio; Madhusoodanan, Nandana; Mansurova, Milena; O’Cathail, Colman; Pearce, Matt; Pesant, Stéphane; Rahman, Nadim; Rajan, Jeena; Rinck, Gabriele; Selvakumar, Sandeep; Sokolov, Alexey; Suman, Swati; Thorne, Ross; Totoo, Prabhat; Vijayaraja, Senthilnathan; Waheed, Zahra; Zyoud, Ahmad; López, Rodrigo; Burdett, Tony; Cochrane, Guy

doi:10.1093/nar/gkab1051

Cited by 77 publications

(56 citation statements)

References 8 publications

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“…Searches may be carried out using a RESTful API or the EBI Search website, returning result sets including hierarchical facets and cross-references to other datasets, allowing links to be followed throughout the available resources. The EBI Search engine provides search functionality to services across EMBL-EBI, including ENA ( 5 ), Ensembl Genomes ( 6 ), the OMICS DI portal ( 7 ) and the COVID-19 Data Portal.…”

Section: Ebi Search and Job Dispatchermentioning

confidence: 99%

Search and sequence analysis tools services from EMBL-EBI in 2022

Madeira

Pearce

Tivey

et al. 2022

Nucleic Acids Research

Self Cite

1,534

915

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The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI’s data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.

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Section: Ebi Search and Job Dispatchermentioning

confidence: 99%

Search and sequence analysis tools services from EMBL-EBI in 2022

Madeira

Pearce

Tivey

et al. 2022

Nucleic Acids Research

Self Cite

1,534

915

View full text Add to dashboard Cite

show abstract

“…If we assume that a HIBF index needs about 40% of the input size, and that we can handle millions of user bins, one can use the HIBF to index very large sequence repositories. For example, the European Nucleotide Archive (ENA) contains currently about 2.5 million assembled/annotated sequences with a total of ≈ 11 Tbp [CAA + 22]. Using the HIBF data structure, we could build 11 HIBF indices, each storing roughly 1 TB of sequence content in about 200, 000 user bins .…”

Section: Discussionmentioning

confidence: 99%

Hierarchical Interleaved Bloom Filter: Enabling ultrafast, approximate sequence queries

Mehringer

Seiler

Droop

et al. 2022

Preprint

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Searching sequences in large, distributed databases is the most widely used bioinformatics analysis done. This basic task is in dire need for solutions that deal with the exponential growth of sequence repositories and perform approximate queries very fast. In this paper, we present a novel data structure: the Hierarchical Interleaved Bloom Filter (HIBF). It is extremely fast and space efficient, yet so general that it has the potential to serve as the underlying engine for many applications. We show that the HIBF is superior in build time, index size and search time while achieving a comparable or better accuracy compared to other state-of-the art tools (Mantis and Bifrost). The HIBF builds an index up to 211 times faster, using up to 14 times less space and can answer approximate membership queries faster by a factor of up to 129. This can be considered a quantum leap that opens the door to indexing complete sequence archives like the European Nucleotide Archive or even larger metagenomics data sets.

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“…The NONCODE database uses public RNA-seq data of human and mouse to estimate lncRNA expression levels. Human BodyMap 2.0 data from 16 human tissues (PRJEB2445) and mouse RNA-seq data set from six different tissues (PRJEB2476) were downloaded from the European Nucleotide Archive [ 40 ]. The expression level unit is FPKM/TPM.…”

Section: Methodsmentioning

confidence: 99%