We are going to try to find all the mammalian osteonectin proteins in Swissprot.
From the
SRS front page, click on the Library Page tab. This takes you to the library select
page. Click on the checkboxes beside UniprotKB/Swiss-Prot (this includes the final Swissprot
versions of a protein entry) and beside UniprotKB/TrEMBL (includes the still preliminary versions that have not yet
been fully annotated). SwissProt and TrEMBL (translated proteins from EMBL) are both subsets of the UniProt KnowledgeBase. We then click on the Standard Query Form box, which takes us
to the standard query page. There are four main text boxes in the center of
the page. Change the pull-down menu of the first one to 'Description', and
type '*osteonectin*' into the text-entry box.
The reason we surround this keyword with wildcards is because in some entries, the osteonectin
keyword is surrounded by braces. The indexing system that SRS currently split words in
the description field by whitespace, so the braces are included in the keyword.
Change the second pull down menu
to 'Organism Name', and type 'mammalia' into the relevant text-entry box. Change
the Result Display Options view box as 'SeqSimpleView'. The UniprotView has more details,
but it is easier to see at a glance what sequences one has when using the SeqSimpleView.
Click on Search.
Show SRS QUERY PAGE image
The query found sixteen entries from Swissprot and TrEMBL.
Twelve of these are osteonectin proteins from Swissprot proper, which include two partial
sequences for pig and mink. Five sequences from Swissprot proper are testican sequences,
which are related to osteonectin. There are also four TrEMBL sequences.
If we look more carefully at these
sequences from TrEMBL, we can see that two seem to be sequence variants of the human
testican 2 sequence, and one is another testican 2 sequence from mouse,
for which we already have full-length proteins. The fourth one appears to be a new
osteonectin sequence from macaque.
We can now save these sequences to a file. Check the boxes beside all the
sequences we want to keep, namely all the full-length, or nearly full-length,
protein sequences from Swissprot, excluding the testican sequences
(a total of five sequences) but including the TrEMBL macaque sequence. By default, as soon as you check a box, the radio button under the
Apply Options To heading changes from 'unselected results only' to 'selected results only'.
Change the 'View Results using' menu under the Display Options heading to FastaSeqs.
Then, click on save. This will take you to
another page where you are reminded how many sequences you are saving,
and what the identities of the proteins that you are saving are. Make sure
the view format is FastaSeqs and that you choose
'File(text)' from the Output To heading. Click on Save.
Show SRS SAVE PAGE image
Your
browser should ask you what you would like to call your file (default on IE5: wgetz),
and where you want to save it. Type 'osteonectin.fasta' and click Save.
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