Frequently Asked Questions

What are primers and how do I identify them in my sequence?

Primers are short strands of nucleotides used to deliminate the start of DNA synthesis, amplification and/or sequencing. Primers can occur naturally as short RNA strands, but for DNA amplification and sequencing experiments they are usually manufactured in a laboratory. These manufactured primers are typically designed specifically for a group of organisms that share similar DNA sequences, but some primers have the ability to bind to a multitude of organismal groups, and are known as Universal Primers.

In DNA barcoding, where only the mitochondrial COI gene needs to be amplified and sequenced, primers are fundamental because they determine the exact portion of the gene that should be targeted during PCR and sequencing. The sequence codes for the primer are available through the manufacturer, and can be easily recognized in the nucleotide code after DNA sequencing is completed.

It is advisable to trim out the primers before aligning and analyzing your sequences. BOLD-SDP has a built-in sequence processor that will identify and trim your primers automatically. Compare the primer sequences provided by the manufacturer with those identified by BOLD-SDP, chances are they match up very well!