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stephenhart 10-11-2011 01:45 AM

comparative genomics with a human pseudogene
I have identified a pseudogene in my human RNA-seq data. I would like to know how well this gene is conserved in (i) other primates and (ii) other mammals. Is the best course of action to put the gene ID through UCSC (i.e., Multiz, Phylop, Phastcons)? Or should I do a multiple alignment myself and then analyze it? I would, of course, eventually like to identify which regions specifically are conserved/derived. Your advice is appreciated.


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