4) Check Oligonucleotides Against Database
The
next step is to screen our oligonucleotide collection to identify
which oligonucleotides best describe our taxon whilst excluding
non-target sequences. The main window now looks as follows:
We click on 'Check Oligonucleotides Against Database' button and the
following display is generated:
The selections we have made so far are summarised in the top half of
the display. There is an option to specify the maximum number of
acceptable non-target records our ideal probe should hit. In this
example, we shall use the default setting of zero. Clicking the
'Search Database Records' button starts the screening process and, once
complete, the following output is displayed:
Of the 576 oligonucleotides we started with, 126 target our target
taxon exclusively. In this example we would like an
oligonucleotide with no degenerate bases and a %G-C content of
50. Sixteen oligonucleotides fit this criteria. We decide
to consider the first of these, oligo number 4 (GCTTGCTTTTTGCTGACGAG)
in more detail by double-mouse-clicking that oligonucleotide.
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