The SRS home page begins with a paw. Clicking on
the Start pad will bring you to a series of databases that you can
interrogate. You can interrogate as many databases at the same time as you
want. These databases include sequence databases, protein domain databases and
mapping databases, among others.
For example, clicking on the box to the left of Swissprot
(in the Sequence set of
databases) implies that whatever query you undertake will be directed
at the Swissprot database.
You can either do a "Quick Search" which allows you to enter a simple query
term, such as "bact*" which will retrieve all sequences from SwissProt that
have the word, or partial word, "bact" in them, i.e. all bacterial sequences,
as well as bacteriophage, and any sequences from any other organism that
have "bact" anywhere in their entries.
However, unless the query you enter is quite specific, you will get a
large number of sequences, which you cannot modify. The "Quick Search" is
useful for cases where you already know the specific sequence,
for example, by accession number, or want to retrieve a large number of
sequences, for example, all the Cyprinus carpio sequences. However, in this
case, it can be difficult to restrict your search to ONLY Cyprinus carpio
sequences.
A much more efficient way of retrieving sequences, once you have chosen
the databases that you wish to be searched, is to click on the "Standard"
button in the query forms box. This moves you to the query page form, which
allows you to submit any particular query you wish, making it as specific
as you want, using a Boolean expression. At the top of the page is a note
of the databases you have selected (in this case, Swissprot). Enter your query
terms into the text-entry boxes provided. You can restrict the search by
changing the drop-down list box to show the specific fields you want searched
with the text you enter into the text-entry box. Separate keywords in
the same box have to be linked by a logical Boolean operator
(default on two or more lines
of the four used is AND). For example, if you wanted to get
all the rodent sequences for alpha tubulin, except those from mouse, you
could enter 'rodentia ! mouse' into the text-entry box, change the 'AllText'
in the drop-down list box to 'Organism', and enter 'alpha tubulin' into the
next text-entry box, and change that drop-down list box to 'Description'.
Finally, click on the "Submit Query" button on the left of your screen.
A new window will appear will the query description at the top.
The results of your query will be presented in table format below. Here, we
found one alpha tubulin gene, from a Chinese hamster, as opposed to the
five entries we would have retrieved if we had looked for ALL rodent alpha
tubulin entries. You can then save these sequences, most usefully,
in FASTA format. Change the "View" drop-down list box from
"SeqSimpleView" to "FastaSeqs", and click on the "View" button.
Click Netscape's File: Save As, and save to your computer hard drive.
The "Extended" query form page has a separate text-entry box for every
field, and allows you to use more than the four boxes available
in the "Standard" query form.
For more detailed instructions on how to use the SRS query system can be found at
the SRS documentation site.
|
