Editing Data - Using the Assembly Panel

The Assembly Panel provides you with the ability to edit the assemblies and consensus sequences produced by the automated steps of Phineus.

The panel itself is made up of several components, namely

The Sample Navigator:

This component contains an explorer-like tree. The first nodes (named samp1-6) correspond to the samples which have been processed. If you expand these nodes you will find a node called 'Assemblies' for each strain/isolate, which contains the genes whose tracefiles have completed processing and are available for viewing and editing.

If a sequence does not appear here, then it may be because the strain/isolates were mislabeled during the list generation, or that the sequence from all the reads in the sample was of poor quality and so was excluded.

To load an assembly, simply click the gene name.

To revert to the sequence that was originally generated by the automated steps, select reload original assembly, if you have previously edited the sequence and wish to revert to that you can do so by selecting reload saved assembly. You can save the assembly in a FASTA file by selecting that option, and you can save your edits by selecting save selected assembly to database. In addition,the system will automatically save the open assembly each time you select a new assembly to view.

It is important, therefore, if you have made edits which you do not wish to be saved, that you select 'Reload Saved Assembly' before chaning the assembly being viewed.

When the sequence is loaded, it is displayed in the Sequence Panel and the Tracefile Panel.

and

You can change any of the bases in the sequence panel, and by selecting a base Phineus will snap to that position on the composite chromatograms. Note that Phineus automatically reverse compliments both sequence and chromatograms for reads in the reverse direction.

In addition, the sequence view has a clickable menu, accessed by left-clicking the mouse when the mouse is over the alignments. This enables you to;

The chromatograms appearance can be modified using the chromatogram control panel:

In this panel you can change the wave length and wave height of all, or some of the trace's, you can scroll one or more of the traces simultaneously. In addition you can have Phineus hide any combination of the traces for A, T G or C.

Once you have completed editing, you can make use of the control buttons

Here you can retreive allele numbers from MLST.net, save the consensus sequences to a file, and/or finish and save your data for later use.

It should be noted that if you are unable to complete editing in a single session, the session will be available at any time until it is marked as finished from the Phineus menu, via the option to 'Resume A Previous Session'. Previous finished sessions can be reviewed via the option 'Review A Complete Session', also located on the Phineus menu.

To edit sequence -

- Select the assembly you wish to edit, and the sequence will load
- Select t the position of interest, and edit it either by entering values from the keyboard, or, by using the editing menu available by right clicking the mouse button.

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