Question: Parameter to consider a hit as a gene copy
gravatar for felipe-bita
2.3 years ago by
felipe-bita0 wrote:

Hi guys, i am trying to identify single copy genes in rice, what i've done so far was blast the CDS against itself and parsing the results with bioperl. My problem now is that i don't know what i use to consider a hit as a gene copy, i am calculating the proportions, alignmentlength/querylength and alignmentlength/hitlength, but what value should i use to define as a copy? I have not found anything in the literature, if someone has information to give me or a better strategy i would be very grateful.

blast alignment gene • 586 views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 2.3 years ago by felipe-bita0

You can use blast e-values to discern homology. If there is homology, there was a gene duplication (or domain shuffling) at some point. However, I am not sure you want to remove ALL duplicated genes, may be only those which duplicated after some point in history (e.g. divergence of rice from another plant species)?

ADD REPLYlink written 2.3 years ago by abascalfederico1.1k
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