i want to test the specificity of degenerate primers for a virus
NCBI does not support degenerate primers so if any one know how can i solve this or how to use De-MetaST-BLAST tool ?
Thank you ...
Eman Bassiony
Dear Yasmeen
You can use a software called geneious: https://www.geneious.com
You need to have your sequence first, then test your primers with geneious.
Although this software is not free, you can download a free trial copy for few days.
Best wishes
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Andrew Jenkins
Blast will accept 'N'. That's the way I usually do it.
You may have to adjust some of the parameters, as the E-value gets quite low for degenerate sequences.
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Vincent Mulholland
I use https://mfeprimer3-1.igenetech.com/spec/
Paste in your degenerate primer pair and set the "Background Database" to Virus genome (EBI).
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Vincent Mulholland
Jojo Redb
There is "NCBI Virus" which is probably equivalent. The number of databases has increased a lot in the last two years. Hopefully that increased choice makes it useful to a wider range of users.
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