Quick Start Guide
- Enter primer set or probe to check. Enter a primer
set or probe in the text
boxes
provided within the main
window. Make sure that all oligonucleotides entered
correspond to the sense
strand of the target nucleic acid, and
that they run from 5'-3'. Use ReverseComplement
to convert antisense oligonucleotides, if necessary. You may also
enter positional
information
relative to the Esherichia
coli 16S rRNA
gene, if that gene is being considered and the RDP
database is to be loaded (this ensures
that only sequence records of sufficient length within the RDP database
are considered).
- Load one or more datasets to check primer set or probe against.
Click 'Load Database(s)' button within the main
window and use the resulting
dialog box to select one
or more datasets that your primer set or probe will be checked against.
- Run the analysis. Press the 'Do Analysis' button
on the main
window - the duration of
the resulting analysis will depend mainly on the size of the database
loaded
and the speed of your computer. For example, ~12,000 records will
take approximately 15 minutes to run on a computer with a 900 MHz
processor.
- View output. Press 'View Results' on the main
window and a results
window is presented. The databases
previously selected are redisplayed, this time colour
coded according to how well
their contents are described by the primer set or probe used.
Identify
the database representing the target group you are interested in (by
clicking
on it with the mouse) and a graph
is
displayed showing what percentage of records within and outside of
that group are targeted by the oligo(s) with increasing number of
mismatches.