Entering edit mode
7.9 years ago
adp7
▴
10
Hi, I want to design primers specific to a gene subfamily (not 16SRNA, protein genes) found in metagenomic data. In order to do that I generated a multiple alignment of my sequences and a file of non target sequences. I'm looking for a command line tool to automatically generate degenerate primers using multiple alignement and non-targets sequences as input. I have done some research but I don't find any software that meets my requirements. A lot of programs are web-based, primers3 don't work for degenerate primers and some tools don't work at all...
Using Hyden and checking for specificity seems the best thing i can do.
Any advice and suggestions will be greatly appreciated
