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.
Previous page | Next page