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SUMMARY

We have used Primaclade successfully to identify primers in alignments of 200-2128 bp length comprising 2-17 species. In general, Primaclade performed best with alignments of up to about eight species and up to 29.0% sequence divergence.

Perhaps not surprisingly, input of a good alignment is vital for useful results with Primaclade. The software is not effective in finding primers in ambiguously aligned regions, nor is it capable of finding primers in alignments with poor consensus. More primers were detected in longer alignments with low sequence divergence, whereas fewer primers were detected in shorter, more divergent datasets. In the case of very divergent alignments, such as the STMADS11 example discussed above, we found it more efficient to partition the alignment into several smaller files and run Primaclade independently on each file.

Primaclade provides a quick, easy, powerful and freely available solution to researchers who want to design PCR primers across multiple species, As such, it will greatly simplify the design of PCR primers for any comparative molecular study.

Introduction | Description | Tests | Summary | References | FAQ | Program Interface