Would any body help me to design overlapping primers for full length amplification of different HCV genotypes especially HCV genotype 3a and 3b ?
Dozens of HCV complete genomes have already been sequenced:
www.hvv.lanl.gov provides complete genome alignments which can be used to identify conserved (good for primers that will bind to all genotypes) regions of the genome as well as the diverse regions (good for making genotype-specific primers or for studying diversity within a sub-genotype lineage).
The HIV Databases has a primer design tool that can work for any DNA, there is nothing special about HIV:
http://www.hiv.lanl.gov/tools/primer/main
But I would highly recommend reading the materials/methods of publications which describe the successful amplification and sequencing of a few of the genomes that have already been done, and finding out if the primers which have already been proven to work well, can also work for you. Re-inventing the wheel, is usually much slower and more painful, than using prior experience.
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