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Multiplicity Graph

 
Figure 2. Multiplicity graph showing all targets to which NC_004331-1408 aligns
(click for full-size image)

Figure 2 is an example output from singleEdges.R.  All query and target sequences are grouped together by chromosome with queries on the left and targets on the right.  All points which are connected by a segment represent an alignment with an e-value at or below the significance threshold.

 


Figure 3. Multiplicity graph showing all alignments generated
(click for full-size image)

Figure 3 shows the total collection of alignments generated by the BLAST search.  This figure allows for a global view of the multiplicity and homology of the alignments.

Each edge represents an alignment with an e-value at least as small as the specified cut-off.  Given the true nature of a query sequence, figure 3 tells us one of three things:  1) If the query sequence is an actual RNA hairpin, the figure could be providing information about the query's potential targets; 2) If the query is from a pseudo gene, the figure could be providing information about a duplicate gene; or 3) if the query is a low-complexity repeat sequence, then the figure tells which targets contain similar repeats.
 
 

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