FSPD Fagment Specific Primer Design

Fragment Specific Primer Design is another primer design algorithm used by PRIMEGENS. This algorithm is used when there is a very long query sequence for which multiple primers are required for its amplification.

This algorithm first break down the whole query sequence into small overlapping fragments, and then, design primers for each of these fragments. For this, user should provide the length of each fragment into which the query sequence will be divided (fragment length) and the distance between two fragments to design associated primers (fragment period).

After the fragmentation of query sequence, this algorithm works exactly similar to the SSPD algorithm to design primers for each of the fragment and give multiple primers for a long query sequence.

FSPD figure

Above figure shows the flowchart for FSPD algorithm.