Sequence retrieval using SRS
SRS is a powerful sequence retrieval system based at the EBI that provides access to many different databases. SRS has many different features and it’s not possible to cover them all here. We’ll just use it to retrieve the same sequence that we retrieved using Entrez in the previous section, to give you a quick look at how SRS works.
Click here to bring up the SRS page.
Step 1: Click on the START area to start an SRS session (show me).
Step 2: You will be faced with quite a complicated looking page - this is the top page. This page allows you to select which database to search. In this case we will use the EMBL database (The EMBL database contains essentially the same sequence information as the GenBank database that we searched with Entrez). Click the box labelled EMBL to tell the system to search the EMBL database and click on the QUERY tag at the top (show me)
Step 3: The query form will now appear. This form lets you define the terms for the search. We want to search for glutamate racemases from Bacillus subtilis. The form has space for 4 search terms. Type the first, Bacillus subtilis into the first text box and the second, glutamate racemase, into the text box below.
Since Bacillus subtilis is the organism we can limit search term one to organism. Change the drop down box next to the first text box to read Organism.
By default the program will just return a list of entry names. We will ask for more details in the search results – Set the drop down list labelled ‘Use predefined view’ to SeqSimpleView
Click on submit query on the left hand side to start the query (show me).
Step 4: You will now see a list of entries from the EMBL database that meet our criteria. The first five a large stretches of the genome but the sixth entry contains the entry for the single gene that we want. Tick the box next to the entry, EMBL:AB003685.
Since we want to see the sequence in FASTA format then we need to change the output format to Fasta. Select the ‘FastaSeqs’ option from the drop down list underneath the View button on the left hand side of the display. Now click the ‘View’ button. (show me)
A page will be displayed showing the nucleotide sequence for the glutamate racemase gene in FastA format. This should be exactly the same as the one we retrieved from GenBank using Entrez so there’s no need to copy and past it unless you forgot last time. (show me)