BLASTX of a query gene shows 5 hits in my subject, how can I find out which of these are expressed and which are pseudogenes (using DNA sequence or by sequence analysis)??
How can sequence analysis establish whether a genomic sequence is a functional gene or a pseudogene?
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$\begingroup$ Perhaps search the EST or TSA database? $\endgroup$– canadianerCommented Feb 14, 2017 at 19:15
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1$\begingroup$ Think for yourself. What types of pseudogene exist? How do they differ from functional genes? If you do not know the answer to this search on the web. When you understand what pseudogenes are some of the answers to your question will be apparent. $\endgroup$– DavidCommented Feb 14, 2017 at 19:53
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There is no good single answer genes which long have been though to be pseudogenes may have function in a very narrow set of cells.
That being said, some of the best indicators are; destruction of the ORF, accumulation of C->T and G->A mutations (methylation/deamination in mammals).
Expression is probably not a good indicator, because once you start including long non-coding RNA, pseudogenes may be transcribed, but may not have a protein-encoding function (if any).
You can also measure loss of introns and a poly-A tail in the DNA sequence which is consistent with a retro-pseudogene, but that doesn't mean that the 'pseudogene' doesn't have it's own function.
Overall, evolutionary conservation is the fastest and most reliable indicator, but ultimately genetic knock-out would be required.
If you have more information about the pseudogene, there may be other useful information which could help distinguish the two.
