I'm trying to clone an invertebrate gene/s using consensus PCR primers
that were designed by comparing cDNAs from a vertebrate gene family. The
approach I am taking is to essentially jump down the phylogenetic tree in
hopes that sequence similarity will be greater between less divergent
phyla and thus give me a greater chance of amplifying genuine product/s.
I would then use this product to design new primers with a bias toward the
lower phylum's sequence.
1. Has anyone used this type of approach before?
2. Does anyone know if there are any codon preference tables for
invertebrates such as the echinoderms or mulluscs?
3. Does anyone have any "better" ideas?
Your help is greatly appreciated,