Question: How to find SSR location i.e whether it is in CDS, or UTR
0
gravatar for majeedaasim
2.4 years ago by
majeedaasim40
United States
majeedaasim40 wrote:

I have identified a set of SSR containing sequences from my transcriptome assembled denovo. I used ORF predictor to predict ORFs from SSR containing sequences. Now I would like to see whether my SSRs are in ORF, 5'UTR or 3'UTR and their relative frequency.

Is there anyway do it?

THanks

location rna-seq ssr • 968 views
ADD COMMENTlink modified 11 months ago by Abhishek20 • written 2.4 years ago by majeedaasim40

Did you find any answer to this? please share. Thanks

ADD REPLYlink written 11 months ago by Abhishek20

Just to be sure you mean "simple sequence repeat" right?

ADD REPLYlink written 11 months ago by kristoffer.vittingseerup3.0k
0
gravatar for lakhujanivijay
2.4 years ago by
lakhujanivijay4.8k
India
lakhujanivijay4.8k wrote:

How did you identified them? Tools generally output the locations as well from which the SSR's were identified.

ADD COMMENTlink written 2.4 years ago by lakhujanivijay4.8k

I identified them using MISA. I have the locations of my SSRs. But the point is how can I relate them to start and stop codons after finding ORFs using ORF predicting tool so that I may know whether it is within CDS or outside. I have a large set of sequences so it is cumbersome to inspect it manually. Is there any tool which can corelate the SSR star/stop positions with the predicted ORF start/stop positions.

Thanks

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by majeedaasim40
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