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Old 02-07-2011, 01:45 PM   #1
archananraja
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Location: Concord

Join Date: Dec 2010
Posts: 3
Question Gene Finding

Hi All,

I am trying to identify genes in a specific pathway from an unannotated draft genome assembly?
Below are the details of what I have:
1.I have identified orthologs for the genes of interest
2.I have also identified the putative gene regions in my assembly


Now,
How do I identify gene duplicates and missing regions in my predicted gene?
I am a little confused because I have a list of nearly 70 genes to identify.


Any help would be greatly appreciated.
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Old 02-08-2011, 06:15 AM   #2
krobison
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Posts: 747
Default

At the most basic, you'll want to use TBLASTN to search the protein sequences of your collection of pathway members vs. the contigs from the reference genome.

Identifying which hits are really the same thing (but from incompletely assembled regions) and which are paralogs/pseudogenes will take a bunch of work. In some cases, mate pair/paired end information may be available to assist in inferring which contigs are near each other in the genome. Similarly, frameshifts and other sequencing/assembly errors are likely to be present & may require close inspection to distinguish biology from artifact.

Ideally, you would have access to DNA from that genome & the resources to do some PCR & sequencing experiments to test hypotheses as to which fragments belong together.
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Old 02-08-2011, 07:25 AM   #3
archananraja
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Smile Thanks

Thankyou....Let me see how it goes.
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