Allows to select the 'PT_SERVER' and its database, to customize
the presentation of the results, define the stringency of target
search and physical characteristics of the probes.
Select a 'PT_SERVER':
Select the appropriate 'PT_SERVER' from the menu
displayed after pressing the button below the
'PT_SERVER' prompt. The 'PT_SERVER' database (*.arb)
has to be consistent with the current. (see 'Main
Topics': 'Probe Design'; 'PT_SERVER What Why and How')
Customize output of results:
Type the number of probe target proposals to be
displayed in the 'PD RESULT' window by typing it to the
'Length of output' subwindow.
Define number of accepted non-targets:
-
Type the number of non-target species which you would
accept to be detected by the probe to the 'Max. non
group hits' subwindow.
-
This helps not to miss potential target sites in case
that species belonging to the particular specificity
group had been overlooked while marking (see: 'Main
Topics': 'Probe Design').
Define number of accepted inter- and intraprobe base pairings:
Type the number of potential base pairings within or
between probe molecules.
!!! Not yet implemented !!!
Define minimum number of target species:
-
Type the fraction (%) of marked species which have to
share the target site to the 'Min. group hits (%)
subwindow.
-
This helps to design multiple probes in case that common
target sites are not present in all species of the
particular specificity group.
Define length of the probe:
Type minimum and maximum number of nucleotides to the
corresponding 'Length of probe' subwindows to define
probe length.
Define dissociation temperature:
A range of allowed dissociation temperatures (= 4xGC +
2xAU; centigrade) can be defined by typing minimum and
maximum values to the corresponding subwindows.
Define the G+C content:
A range of allowed G+C fractions (%) can be defined by
typing minimum and maximum values to the corresponding
subwindows.
Define target region:
-
A preferred sequence (alignment) region can be defined
for the probe target sites by typing the nucleotide
numbers of the homologous positions within the E. coli
molecule.
-
This requires:
-
Your (pt_server) data is aligned.
-
There is a SAI named 'ECOLI' which
includes the reference sequence.
Press the 'EXPERT' button to display the 'PD SPECIAL' window if
base pairings should be individually weighted (see ´Weighting of Base Pairings´).
Press the 'GO' button to start the calculations.
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