Our final example illustrates how AlignmentViewer's animation capabilities can be used to show the history behind the investigation of the HIV sequence. The idea is to study the entry dates of sequences related to HIV.
Figure 8: HIV's alignment report animated with position, score, frame,
and entry date mapped onto the X, Y, Z, and time axes, respectively.
The amount of sequence information related to HIV grows
rapidly. ('81: diagnosis of AIDS, '82 to 85: HIV linked to AIDS,
'86: HIV gained international attention, '89: large grants supporting
HIV research.)
Figure 8 uses AV's accumulative play feature, showing the information gathered on HIV from 1979 to the present. Position, score, frame, and entry date are mapped onto the X, Y, Z, and time axes, respectively. The glyphs represent the composition of each alignment horizontally, since position is mapped onto the X axis. The animation moves smoothly over all years, but only certain representative frames appear in this figure. The representative frames begin with 1979 (the date of the first database entries). AIDS was first diagnosed in 1981, and the frame for that year provides evidence of this discovery. Research between 1982 and 1984 revealed HIV to be the causal agent of AIDS, and an increase in the number of alignments occurred in 1985. A larger increase in the number of alignments occurred in 1986 when HIV gained international attention. Still another large jump happened in 1989, shortly after the U.S.\ government provided large grants for HIV research. The first automated sequencing machines were also put on the market around 1989. The last frame shows the current state of information related to HIV, displaying all 6692 alignments to the GenBank database. The HIV textual report for these alignments is roughly 3200 pages. In [6], we demonstrated how AV revealed high-level features in the HIV report that were previously hard to find. We also showed how the detailed information on each alignment is either represented by the comb glyph or provided by hyperlinks to the original textual report.
This animation provides a glimpse into the history of information related to HIV. It also illustrates the growth of the sequence databases. GenBank [5], the primary repository for DNA sequence data, contains roughly 463,800,000 bases in 686,000 sequence records as of February 1996, and is doubling every 14 months.
We demonstrated how our system visualizes the history of HIV and the growth of the accumulated sequence data related to HIV as a short animation. These techniques have proven useful in our analysis, and provide evidence of the power of the combined technique.
