Reviewing Data In Phineus

Phineus provides several tools to allow you to edit, review, export and analyze your stored data.

To access these features, select 'View and edit old data' from the 'Analysis' menu

This will bring up the Data Review window

There are three ways to view and search your data, which can be selected by clicking the relevant TAB -

	Basic Search	Allows searching based on simple strain parameters and allows profile data to be returned.
	MLST search	Allows searching for Strains or STs, based on similarity to a chosen ST
	Strain Search	Allows the DNA sequence to be returned based on a 'basic' search'

To use the Basic Search, first select the field in your data you wish to search

The search options will be different depending on the MLST scheme you are using. For the following example we will search on 'Strain name'.

Select the Project that you wish to search.

You can then enter a search term. The system will automatically look for all values (in this case names) which contain the word or phrase which you enter.

If you wish to see the whole database, enter the wild card ' %'. This will allow all the entries for that project to be viewed.

Once you have entered the search term, press search.

The results will then be loaded in the two panes located below the search bar.

The left pane contains a unique list of all of the ST's present in your search, while the right pane contains the profiles for the strains which have been returned.

The table in the right pane has a number of options, which can be viewed by pressing the right mousebutton.

The first option on the list is 'View Sequence Data'. This allows you to view the most recent assemblies generated for each gene in the selected strain. Selecting this will produce a similar view to the one you see in the editing step of tracefile processing.

This interface operates in the same way as the interface to the editing step. To view and edit sequence simply click on the gene of interest. Saving, and reverting to the saved gene are achieved in the same way as with the editing steps. If you wish to review these, you can do so here.

The only major difference with this view is that there is a new button located below the list of genes, for retrieving allele numbers. This operates the same way as the button in the main editing step.

The next options on the list all save data to a file specified by you.

You can export the profile for the selected strains/sts, all strains/sts or you can export the sequence (either concatenated or in an Excel/Access readable comma separated format). When you select one of these options, you are presented with a save dialog

Simply navigate to the directory where you wish to save your file, and supply an appropriate name, before clicking 'Save'.

Phineus also allows you to view your data using eBURST (for further details see http://eburst.mlst.net) accessable through the eBURST submenu.

Here you can select to view your local data on its own, or compare it to the full database located at MLST.net.

When you select one of these options, eBURST will open

For more information on using eBURST, see the eBURST website at eburst.mlst.net or click here to download the eBURST readme file

You may also want to edit data present within the database. To do this, you will need to tell the program that the table is editable.

Once you have done this, and made your changes you can either Save, or Undo the changes.

Finally, you can check to see whether your Sequence Type is found in the public MLST database for all strains selected. This currently uses a copy of the MLST database which is stored locally, on your PC, which is updated automatically (Full details of updates will be made available here shortly.)

You can also view the other information for selected strains by pressing the button marked 'Get Details for Selection' . This will then produce a table in the bottom window containing all other data stored for the strains of interest.

This table also has a menu (right-click), and you can edit the values located here using the same method outlined above.

The second search offered is an 'MLST' search, where you can search for similar strains or STs by their allelic profile.

To begin select the schema that you wish to use.

When you select 'Use Schema' the program will determine the projects associated with that schema.

You should then decide if you wish to search by Strains or by STs. Both operate in a similar way. In this example the user is searching by ST, to find other STs with profiles similar to ST 1 at all 7 loci.

The result is shown in a tabular form. By selecting one, or several of the ST profiles which are displayed in the right hand table, you can view the details of all of the strains which share the selected STs.

To do this, once you have the ST(s) of interest highlighted, select 'Get Details for Selection'.

If the search is repeated, searching for strains instead of ST's

Then the table produced contains strain details

and selecting 'Get Details for Selection' will display the strain details as it does in the Basic Search.

The MLST search offers the same menu options as the Basic search.

The final search option allows you to display sequence in the results of your search. To do this, select the search field, and the project to search (as in the case of the basic search) and provide a search term

You will then obtain a table containing the strains of interest and the sequences for each locus

You can export these by selecting the rows of interest and copying by pressing <Control>-C. You can then paste this into any text editor, where the table will appear in a tab delimitated format.

If you wish to export sequence to Excel or Access, then it is recommended that you export the sequence in a comma delimitated file, from the table produced by the basic search.

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