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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