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European Nucleotide Archive Data Search and Retrieval Nicole Silvester www.ebi.ac.uk/ena.

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Presentation on theme: "European Nucleotide Archive Data Search and Retrieval Nicole Silvester www.ebi.ac.uk/ena."— Presentation transcript:

1 European Nucleotide Archive Data Search and Retrieval Nicole Silvester

2 Objectives Understand the different types of data available from ENA Know how to find/download them

3 Data available from ENA Metadata (XML or tab-separated text) Flat files Sequences (FASTA) Raw reads (FASTQ or submitted format) Analysis (submitted format)

4 Searching for data By accession By taxon By search conditions: Text search Advanced search By sequence: Sequence search

5 Accession entry point Retrieve XML format Retrieve Flat file Retrieve FASTA sequence

6 Taxon entry point NCBI tax ID Scientific name Retrieve FASTA sequences uence_release&offset=1&length=1000&display=fasta&download=fastahttp://www.ebi.ac.uk/ena/data/view/Taxon:6643&subtree=true&portal=seq uence_release&offset=1&length=1000&display=fasta&download=fasta

7 Text Search vs Advanced Search Text search: “full text” search terms searched against data files searches across all ENA data domains Advanced search: “field-based” search search against specific meta-data fields searches within chosen ENA data domain

8 Text Search vs Advanced Search want: human sequences

9 Text Search vs Advanced Search want: human mRNA sequences

10 Sequence Search

11 Resources


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