3) Find Oligonucleotides

We next want to identify all possible oligonucleotides that could target our taxon.



Selecting 'Find Oligonucleotides' from the main window generates the following dialog box:



We need to select those sequences within our target taxon we wish to design our oligonucleotides from, by checking the tick boxes in the 'Design from' table colum.  In this example our taxon contains ten records: since this is a relatively small number, and we believe all to be reliable, we select all ten. 

Note: If our taxon had been much larger we might have considered selecting some representatives of the available records only (say, no more than 15), as designing oligonucleotides from too many sequences, especially if the sequences are of variable quality, can result in missing the most useful oligonucleotides.  For example, it may not be possible to identify an oligonucleotide that can unambiguously match all members of the target taxon whilst excluding all non-target sequences.  A compromise might be necessary between the percentage of target records matched and percentage of non-targets excluded.

In our example we require a 20 base probe, with no more than two degenerate base positions, so we set the oligonucleotide parameters accordingly.  Then we press 'Find Oligonucleotides', and the following results are displayed.


Happy with this result, we select 'Accept' and proceed to the next step.

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