SPADS
SPADS (Specific Primer and Amplicon Design Software)
is a tool for the design of specific GSTs (Gene Specific Tags). From a gene
for which the intron-exon structure is known (or predicted), the program
selects, by comparison to the whole genome, the least conserved region(s),
and designs a primer pair specific to that region for its amplification.
It can be useful to avoid cross-hybrization events in transcriptome experiments
such as microarrays, northern-blotting or RNAi. It is also possible to design
specific primers for your personal PCR / RT-PCR experiments. SPADS uses
a database for checking specificity on Arabidopsis genome, but others databases
corresponding to other genomes or multigenic families can easily be added.