3.1 Searching SRA via the Web
Frequently users want to find records for a specific organism. On the web, the traditional way to do this is via a query using entrez syntax.
Begin by navigating to the NCBI SRA web page, https://www.ncbi.nlm.nih.gov/sra/
In the search bar, enter the following and submit the query
"Salmonella enterica"[organism]
How would you find the correct organism name for an organism of interest?
Another frequent need is to find records derived from a particular sequencing technology. Enter the query below into the search bar and submit it.
"platform illumina"[Properties]
Entrez queries can be combined using logical operators, AND or OR, and parenthesis can be used to structure the statement. Use the query below to find Illumina records submitted as S. enterica.
"Salmonella enterica"[organism] AND "platform illumina"[Properties]
Typically you will want to examine at least some of the results from a web based search individually to see additional information about the records returned. There are generally two approaches available.
Click on one of the records from the previous query results to see a page similar to the one below.
Is the same information available for every record? What other records may be linked?
From the Entrez record, click on the run accession at the bottom to view the record in the SRA Run Browser. You should see a page similar to the one shown below.
What different information is available?
From the Run Browser page, click the analysis tab near the top of the page. This shows the results of the SRA Taxonomy Analysis Tool (STAT), a k-mer based method of estimating taxonomic content of sequence data. You should see a page similar to the one below.
Do the STAT results agree with the submitted organism?