multiPrime is a mismatch-tolerant minimal primer set design tool for large and diverse sequences (e.g. Virus). Here is a web-based version (test: http://multiPrime.cn))
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If a primer dose not work in the final primer set, how to replace it? #1
Generally, primer pairs in the final primer set works well. If a primer pair dose not work or you want to add primer pairs into your primer set, you can select a different candidate primer from the same cluster, which can be found in the Clusters_cprimer directory. Suggestion: before selecting a new primer pair, it is recommended to filter the pair (dimer examination) using finDimer.py in the script directory.
You can refer to a bash file called "select.nondimer.primer.sh" that is located in the script directory. This file can guide you through the process of selecting a new primer and replacing non-functional primer in the old primer set.
Generally, primer pairs in the final primer set works well. If a primer pair dose not work or you want to add primer pairs into your primer set, you can select a different candidate primer from the same cluster, which can be found in the Clusters_cprimer directory. Suggestion: before selecting a new primer pair, it is recommended to filter the pair (dimer examination) using finDimer.py in the script directory. You can refer to a bash file called "select.nondimer.primer.sh" that is located in the script directory. This file can guide you through the process of selecting a new primer and replacing non-functional primer in the old primer set.