Viewing the Results
a) Results Page
After selecting a pre-computed comparison, or generating your own, a page
will be displayed which presents an overview of the
selected sequences, mirroring the view that will be displayed using
ACT. Should you have selected full genome sequences, the difference in
genome size will be mirrored in the scaled overview. Should you have
selected a specific gene, its position will be highlighted with the
selected flanking regions.
Figure 1. Overview of the selected sequences.
b) View Options
A number of options are available from the results page prior to launching ACT.
Open overview in separate window
The overview figure shown above will be opened in a separate browser window
when this option is selected. This can be postioned on the screen alongside
the ACT window to act as a reminder as to the order of the selected
sequences (which is not readily available within ACT), and the relative locations of any selected genes.
Show hits outside selected sequenece (pre-computed comparisons only)
When a displayed comparison is not based around full-length sequences, by
default blast hits will only be displayed when the query and hit regions
from both sequences are within the selected sequence range. Should a hit be
present in the selected region of one sequence, but the hit region is
outside the selected range of the target sequence, this hit is not
displayed. By selecting this option, hits which are 'out of range' for one
sequence are shown as being present with at the first or last base of that
sequence, to indicate that a hit is present to a displayed sequence region,
but not visible on other sequence. These hits will appear as 'triangles'
pointing into the corners of the comparison with the ACT window.
Changing the blast cut-off value. (pre-computed comparisons only)
A blast e-value is a measure of the number of times a hit with particular
score will occur by chance. By increasing the e-value cut-off of the displayed
results, the number of hits displayed will increase, but there is a greater
chance that some of the hits have occurred by chance, and are not
biologically relevent. Reducing the e-value cut-off has the opposite
effect. To change this parameter for 'on-the-fly' comparisons, see section
5 on changing blast parameters.
Providing you have JAVA installed (see
software requirements here), the first time you click ‘Start
ACT’, the stand-alone version of ACT will be installed onto your
machine and the sequence and comparison files streamed for immediate viewing.
Subsequently, each time you launch ACT from within WebACT only the selected
sequence and comparison files will be downloaded and launched for viewing
with the previously down-loaded version of ACT.
After clicking 'Start ACT', a‘File Download’ panel appears.
Click ‘Open’ to
launch ACT and view the genome comparison.
A progress bar indicates the loading
of the sequences into ACT.
If selected, the overview window will also be visible,
allowing the sections of interest to be found easily within the ACT diagram.
For full instructions for using ACT please see the user manual at the ACT homepage
- Click here
A five-way ACT comparison with overview window.