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 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.