1. Data Search and Retrieval
European Nucleotide Archive
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 http://ebi.ac.uk/ena/data/view/<ACCESSION>
Retrieve XML format
Retrieve Flat file
Retrieve FASTA sequence

6. Taxon entry point Retrieve FASTA sequences NCBI tax ID Scientific name
Scientific name
Retrieve FASTA sequences
uence_release&offset=1&length=1000&display=fasta&download=fasta

7. Text Search vs Advanced 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 http://www.ebi.ac.uk/ena/about/browser