Design primer for a family of bacterial genes

Question

[David]

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 ?

Answer 1

[natasha.sernova]

See my answer within this post.

C: Designing primers for family of genes

It also has a bacterial part.