You have spoken and we have listened. For a while now, we have seen requests for a primer tool that is capable is designing primers that are specific to the input PCR template. NCBI has just recently developed such a tool, Primer-Blast, and we have just finished incorporating it into DNASIS SmartNote!
DNASIS SmartNote users now have the ability to select an organism by name or taxonomy id when utilizing the Primer-Blast tool. The tool will design the primers and blast them against the specified genome. The blast results are then analyzed to filter out primer pairs that can cause amplification of targets other than the input template ensuring that the primers you get will be specific.
DNASIS SmartNote users can then easily extract these primer sequences for downstream analyses such as the IDT Oligo Analyzer which includes a Homo-Dimer Analysis as well as some specifications of the oligo which include molecular weight, extinction coefficient, and much more.
For those that are new to DNASIS SmartNote, all your results and sequences are automatically saved for you in your electronic bioinformatics lab notebook so that you can access the information whenever you like and where ever you have an internet connection.
Here is a preview of one of the pages from my SmartNote notebook showing the Primer-Blast and IDT Oligo Analyzer results utilizing the share feature.
Here are some sample screenshots of the Primer-Blast results from the DNASIS SmartNote application: