Hello, I have a family of bacterial genes that are conserved. I have almost 3000 genes for that particuar family.
I would like to design pcr primers for sequencing amplicons for that particular family. On average the sequences are 600nt long and i want to find primer pairs for the miseq platform (roughly 2*250 = 500pb). Ideally the primers should amplify in between 440 and 500 nt.
What is the best strategy. ?
I have first created an alignment of the 3000 genes but don´t know how to move forward from there . I have used degeprime to create degenerated primers from the alignment.
Any iodea on how to move forward ?