Downloading sequence data

Click on the Download Sequence link in the left panel - the rest should be reasonably self-explanatory. You can specify which sequences to download , by selecting one or more project or search lists. There are options for output format, and you can restrict the number of sequences downloaded if you just want to have a look

Retrieving sequences and keyword searching

In the top search bar, choose Sequences from the Search dropdown, and enter all or part of an accession, keyword, or keyword phrase in the For field then click Go. Examples : 

CS44.161106CS4401259600001         # EST contig accession
CS4401259600001                    # part of an EST contig accession - this will also find the ORFS derived from this sequence
interferon regulatory              # keyword phrase
%interferon regulatory%factor%     # keyword phrase with wildcards
AAI31733                           # NCBI accession that may have been hit in a blast search

Running a blast

Click on the AgResearch BLAST link in the left panel - the rest should be reasonably self-explanatory. Hits are hyperlinked back to the database so that you can access sequence , see any other details of interest etc. We can add additional blast options and databases as required.

What possum contigs have hit this sequence ?

Choose Sequences from the drop down list and enter the sequence accession (without version number) - e.g. EAW52797 This will show a graphical view of the queries that have hit this contig - i.e. http://www.possumbase.org.nz/cgi-bin/possumbase/fetch.py?context=default&obid=NCBI.AAI31733&target=ob You can also click through to a report of all queries that have hit this , by clicking on the middle sequence icon . in the glyph labelled Database Search Result, in the information map section

How do I get the EST sequences in a contig or the contig sequence for an EST

The alignment of ESTS making up a contig is displayed in the graphical feature view on the contig page. To click through to the EST sequences themselves - which are also in the possumbase database - the sequence page for contigs and ESTs includes a glyph in the information map titled contig location.On a contig page, click on the second sequence icon in the glyph to list the member ESTs. On an EST page, clicking on the second sequence icon takes you to the page for the parent contig. The Underlined "contig location" link in the glyph will display a page with details of the location record that includes limited information about the contig build - this is not so useful.

How do I link to sequences in the database

Here is an example of a link to a sequence in possumbase :http://www.possumbase.org.nz/cgi-bin/possumbase/fetch.py?context=default&obid=CS44.161106CS4401259600001&target=ob 

What blast runs have been done and when?

In the top search bar, choose Sequence Database Searches from the Search dropdown, and enter * in the For field then click Go.
Clicking on a link will open a page with details about the search.  From there you can click through to information about the database searched or the protocol used, such as masking and blast parameters, by clicking on the biodatabase or bioprotocol icons in the information map.
You can also download all the hits by clicking on the Database Search Result link in the information map, however it is probably better to use the blast search report page noted above.

What databases have been searched ?

Choose Sequence databases from the drop-down list in the main search panel. From the page for a database, there are links to all the searches that have been done against that database.