Thanks for your interests. The problem was solved. The paralogs can be treated as known variants, since the 454 amplicon analyzer supports this functionality.
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As requested, I re-posted the question I asked earlier (I didn't save the exact copy, just try my best to rewrite the question):
I am studying the association of genetic variations within a gene family to certain phenotypes, and is planning to speed up the screening process with 454 amplicon sequencing. But I don't know if I should treat each paralog as a reference sequence or as known variants. The paralogs are highly similar at sequence level, with a few point mutations and small indels.
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As requested, I re-posted the question I asked earlier (I didn't save the exact copy, just try my best to rewrite the question):
I am studying the association of genetic variations within a gene family to certain phenotypes, and is planning to speed up the screening process with 454 amplicon sequencing. But I don't know if I should treat each paralog as a reference sequence or as known variants. The paralogs are highly similar at sequence level, with a few point mutations and small indels.
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