The possible frames are the following
In
the Input Frame there are four radio buttons (only the first one is enabled
in applet mode) that allow the choice of the input sequence (in FASTA or
GenBank text format), possibly by writing in some input windows:
1.
Input from window: When selected, the input sequence should be put in the
nearby window (either by direct writing or by copy-and-paste) and confirm
by depressing the pushbutton "Ok W".
The
Graphic Frame allows to select a tract of the sequence being examined,
and is made of three horizontal bands, i.e., from below, the Sequence Band,
the TR Band, and the Consensus Band.
Whenever
possible, the Sequence Band displays the sequence tract being observed,
while each result, i.e, the TR with the associated consensus, is
displayed in the two upper bands, as explained later.
The
TR Band is a cartesian plane, in which each result is represented by a
horizontal red segment (with a central black dot), having as ordinate the
length of the consensus, and as abscissas the positions along the
sequence. The scale of the ordinates is an approximately logarithmic piecewise-linear
scale, while the scale of the abscissas is a linear scale simply indicated
by its extreme values along the sequence and by a representation of the
scale unit length.
The
Consensus Band is a rectangular area where only the ordinate matters, being
the score of the result; in this area a consensus relative to a given result
is represented as a vertical rectangle whose height is the score of the
result and whose horizontal position is arbitrary (i.e. suggested only
by graphic convenience) but with a straight line connecting the consensus
with the corresponding red segment in the central band.
Within
the rectangle the nucleotide bases of the consensus are represented by
coloured slices (according to the selected colour option, see below), and
are ordered from above (a similar slicing is used to represent, the nucleotide
bases of the tract in the Sequence Band).
Whenever
possible, the TR initial position is displayed above the rectangle, while
the consensus length and the score of the result are displayed below the
rectangle (we note that these three numerical values are also shown in
analog form in the graph).
When
many consensus are shown in the Consensus Band the width of a rectangle
is smaller if the score is smaller.
We
note that while all results for the considered tract are shown (possibly
indistinguishably superposed) in the TR Band, only a limited number of
consensus can be displayed in the Consensus Band.
More
generally elements are displayed only if they are not too small and if
the space is sufficient.
Zoom
or translation actions can also be performed by suitably depressing keyboard
or virtual pushbuttons. As explained in detailed by depressing the Help
pushbutton, eight actions can be performed, namely left or right translation,
go to sequence start or end, zoom in or zoom out by a factor 2 or 10.
The
detailed description of each result can be obtained by clicking within
the corresponding rectangle in the Consensus band, while the detailed description
of the results showed in the frame can be obtained by clicking the Show
pushbutton.
The
details of all the results can be obtained by clicking the Full pushbutton
in the Basic Frame.
When
the penalty becomes stronger, the cumulated length of the DNA tracts that
are considered TR decreases, while it can be easily shown that their number
could increase or decrease, depending on the sequence.
Similar
considerations apply to a growing score and to a decreasing max_gamma.
A
larger max_gamma, or a smaller score, or a milder penalty, markedly increases
the execution time, can require larger dimensions, and might increase the
amount of (possibly non-interesting) output.
On
the other hand the main drawback of a smaller max_gamma, or of a
larger score or of a stronger penalty is the risk of not detecting some
possibly interesting TR.
We
note that the need of long work arrays depends on the degree of repetitiveness
(and not on the length) of the sequence.
In
general terms a lower value for a dimension parameter reduces the memory
requirement and often increases the execution speed, but could be insufficient;
in this case a message is issued suggesting an increase of the relative
value to repeat the search.
We
note that too large a value may cause the Java interpreter to run out of
memory, an error that JSTRING tries to catch, and in this case a warning
message is issued, suggesting to re-run JSTRING after quitting (since after
an OutOfMemoryError the Java Virtual Machine risks to become unable to
manage the garbage collection). This must be done with smaller dimensions
parameters, or, in the application case, by allocating more memory to the
process, i.e. specifying a larger maximum heap size for the Java interpreter.
Default
values used by JSTRING are generally sufficient.
In
the Message Frame a message, context dependent, is displayed in a window,
as in the example below.
label
of
pushbutton |
keystroke
shortcuts |
explanation |
Quit | [ESC], q | quit |
Save | s | save on disc |
Cont | [ESC], c | exit from Message |
Exit | [ESC], e | exit from Help |
Ok W | accept Input | |
Ok D | input sequence by dialog window | |
Ok F | input sequence by file name | |
Ok U | input sequence by URL name | |
Esc | [ESC] | reject input |
Help | ?, h | help about buttons |
Stop | [ESC], s | stop current operation |
Opt | o | change options |
Grph | g | results graphical |
Shrt | s | tabular results |
Full | f | full results |
Run | r | start TR search |
Back | [ESC], b | exit from graph |
Clic | c | help on sensitive graph |
Prnt | p | graphical print |
< | [LEFT], < | left movement |
Home | [HOME], a | sequence begin |
> | [RIGHT], > | right movement |
End | [END], z | sequence end |
- | [DOWN], - | zoom out * 2 |
--- | [PGDN], 1 | zoom out * 10 |
+ | [UP], + | zoom in * 2 |
+++ | [PGUP], 9 | zoom in * 10 |
Show | s | show page results |
Set | s | set option |
Load | l | load sequence |
Beep | b | check during waiting |