Table of Contents
Once BayesFold has finished processing your alignment, it will display the following results screen:
This screen displays the following elements, which are discussed in greater detail elsewhere:
Results caption. The name of the alignment being viewed is presented, along with the number of sequences it contains and its temperature.
Structure drawing. The currently-viewed sequence is drawn threaded though the currently-viewed structure. The IUPAC consensus sequence (see Section 2, “Understanding Consensus Sequences”) is selected by default, as is the structure with the highest overall probability.
Handle of the format palette. The format palette presents options for altering the appearance of the structure drawing; clicking this handle makes the palette visible.
Drawing caption. The current sequence label, structure number, corresponding energy, and alignment name are shown below the drawing.
Sequence list box. This list box contains a list of the sequence labels. The label of the currently-viewed sequence is displayed. Selecting a different sequence label from this list changes the currently-viewed sequence.
Structure list box. This list box contains a list of the structure labels. The label of the currently-viewed structure is displayed. Selecting a different structure label from this list changes the currently-viewed structure.
Important
BayesFold presents only the 100 most likely structures of those it tests for the alignment.
Current sequence. This box displays the currently-viewed sequence.
Current structure. This box displays the dot-bracket format representation of the currently-viewed structure.
Motif text box. Motifs defined by the user may be entered in this box, applied, and then colored on the structure drawing.
Data table display buttons. These buttons control the display of the sequence and structure data tables. Click on the appropriate button once to display a table, and a second time to hide that table again.
If you have folded a single sequence, you may get the following warning message: ATTENTION: BayesFold's probability calculations are optimized for multiple sequence alignments. Since the current alignment has only a single sequence, you may wish to sort the structures by energy rather than by probability. Most of BayesFold's calculations rely on comparisons between different sequences. For a single sequence, the only source of information is thermodynamic folding. Because BayesFold tries to find the best-supported set of base pairs rather than the minimum free energy structure, it will often assign a higher probability to a structure with fewer base pairs, even if forming additional base pairs would lead to a lower-energy structure.
In this circumstance, you may want to sort the structures by minimum free energy instead of by probability so that the base pairs are closed. We should note that, in tests with single tRNA sequences, BayesFold's probability measure actually produced structures significantly closer to the true structure than did minimum free energy folding; however, no structure prediction method is very accurate on a single sequence, and including even one additional related sequence dramatically improves the predictions (provided that it folds into the same structure).