European Nucleotide Archive in 2016

The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) offers a rich platform for data sharing, publishing and archiving and a globally comprehensive data set for onward use by the scientific community. With a broad scope spanning raw sequencing reads, genome assemblies and functional annotation, the resource provides extensive data submission, search and download facilities across web and programmatic interfaces. Here, we outline ENA content and major access modalities, highlight major developments in 2016 and outline a number of examples of data reuse from ENA.

[1]  Pelin Yilmaz,et al.  The SILVA ribosomal RNA gene database project: improved data processing and web-based tools , 2012, Nucleic Acids Res..

[2]  Julian Parkhill,et al.  The Citrobacter rodentium Genome Sequence Reveals Convergent Evolution with Human Pathogenic Escherichia coli , 2009, Journal of bacteriology.

[3]  G. Cochrane,et al.  The International Nucleotide Sequence Database Collaboration , 2011, Nucleic Acids Res..

[4]  The Uniprot Consortium,et al.  UniProt: a hub for protein information , 2014, Nucleic Acids Res..

[5]  David L. Wheeler,et al.  GenBank , 2015, Nucleic Acids Res..

[6]  Lukas Wagner,et al.  A Greedy Algorithm for Aligning DNA Sequences , 2000, J. Comput. Biol..

[7]  María Martín,et al.  UniProt: A hub for protein information , 2015 .

[8]  Toshihisa Takagi,et al.  DNA data bank of Japan (DDBJ) progress report , 2015, Nucleic Acids Res..

[9]  Giovanna Ambrosini,et al.  The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools , 2014, Nucleic Acids Res..

[10]  Hsien-Da Huang,et al.  RNAcentral: an international database of ncRNA sequences , 2014, Nucleic Acids Res..

[11]  Marco Brandizi,et al.  Updates to BioSamples database at European Bioinformatics Institute , 2014, Nucleic Acids Res..

[12]  Tareq B. Malas,et al.  Comprehensive Evaluation of Toxoplasma gondii VEG and Neospora caninum LIV Genomes with Tachyzoite Stage Transcriptome and Proteome Defines Novel Transcript Features , 2015, PloS one.

[13]  Nuno A. Fonseca,et al.  Expression Atlas update—an integrated database of gene and protein expression in humans, animals and plants , 2015, Nucleic Acids Res..

[14]  Eric Delwart,et al.  The Ancient Evolutionary History of Polyomaviruses , 2016, PLoS pathogens.

[15]  Guy Cochrane,et al.  The International Nucleotide Sequence Database Collaboration , 2011, Nucleic Acids Res..

[16]  Emily S. Charlson,et al.  Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications , 2011, Nature Biotechnology.

[17]  Ning Ma,et al.  BLAST: a more efficient report with usability improvements , 2013, Nucleic Acids Res..

[18]  Leif Andersson,et al.  Identification of the Long-Sought Leptin in Chicken and Duck: Expression Pattern of the Highly GC-Rich Avian leptin Fits an Autocrine/Paracrine Rather Than Endocrine Function. , 2016, Endocrinology.