NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.

SRA Knowledge Base [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2011-.

  • This publication is provided for historical reference only and the information may be out of date.

This publication is provided for historical reference only and the information may be out of date.

Problems Searching SRA

Created: ; Last Update: March 18, 2014.

Estimated reading time: 2 minutes

Why don’t I get results when I search for Black Mustard (Brassica nigra) data? How do I find black mustard data in SRA?

Below are two negative search scenarios for black mustard that may describe why you are not getting results:

Scenario # 1: Although the publication you read does not provide SRA accession numbers, it does provide sequencing details that lead you to believe the author may have deposited the data in the SRA, yet when you look for the data in SRA you can’t find it.

Frequently, when SRA accessions are not included in a paper, it is because the data was not actually submitted to the SRA — it was submitted to another NCBI resource (e.g. GenBank or others) instead. So if you get a negative result for a particular search in SRA, try searching other NCBI resources for the sequence data.

Scenario # 2: Often, when you search for SRA data for a particular species one day, you won’t find anything, but the next day you perform the same search, and you might get 150 data records. The reason this happens is that there will be a long period where no one submits data for a particular species, and then a research group completes a project and submits all of their data to SRA at one time.

You can use Entrez and “My NCBI” to set up an automated periodic search of SRA for the term “black mustard” (or “Brassica nigra”) that will notify you when updates to this search are available:

a.

Go to the Entrez SRA page.

b.

Enter your search term in the text box at the top of the page. (e.g. black mustard or Brassica nigra)

c.

Click on the “Advanced” link.

d.

Go to the “Search Builder” section of the response page.

e.

Activate the drop-down menu that contains the words “All Fields” and select “Filter”.

f.

Click on the “Show Index” link to generate a pop-up menu that lists all available filters for SRA.

Note: Only GEO DataSets and Genome currently provide an SRA filter and support email updates. BioProject, dbGaP and BioSample currently do not support email updates. For those resources that do not support email updates, you will have to perform a manual search for new studies/projects that contain SRA data in these resources and scan the results of your search for new studies yourself.

g.

Scroll down the list (which is arranged alphabetically), select either sra gds or sra genome, and click on the “Add to Search Box” button. This will place your selected filter in the search box at the top of the page.

h.

Click the “Search” button.

i.

Once you have the response page listing all the GEO DataSets containing SRA data, click on the “Save Search” link to go to “My NCBI”.

j.

Sign in to My NCBI or register for a My NCBI account by clicking on the “Register for an account” link. Help for My NCBI is available online.

k.

When the My NCBI “Saved Searches” page appears, click the “Save” button to save your search and generate a response page asking for your search settings.

l.

Fill out the response page, which will allow you to select how often (monthly, weekly, daily) you want an update showing new results for the search you just conducted sent to an email address you provide.

You may also perform this search programmatically using Eutils.

I searched SRA using a specific term but don’t get any results. Are there other ways of looking for SRA data associated with that search term?

Try using your search term in either BioSample or BioProject and check your results for links to SRA experiments. If this doesn’t work, try using Eutils.

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