Primerize: software for designing primers for rapid RNA synthesis

Stanford researchers have developed an algorithm and web server to accelerate the synthesis of DNA and RNA molecules. Many modern medicine applications require 'on-demand' templates for DNA genes. The Primerize software is an archive of Python code that is able to design forward (sense) and backward (anti-sense) primers for PCR assembly of such templates using a novel dynamic programming algorithm. The method keeps each primer under a prescribed length and minimizes their total length, effectively reducing the synthesis cost. Primerize has been optimized to reduce mispriming (a significant issue which can lead to the transcription of undesired products) through the avoidance of primer boundaries that could potentially anneal to incorrect sequences. These resulting primers have been tested through the synthesis and purification of templates for in vitro transcription of RNA sequences of up to 300 nucleotides.

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