Question: How to find SSR location i.e whether it is in CDS, or UTR
0
gravatar for majeedaasim
17 months ago by
majeedaasim30
United States
majeedaasim30 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 • 650 views
ADD COMMENTlink modified 17 months ago by Vijay Lakhujani4.0k • written 17 months ago by majeedaasim30
0
gravatar for Vijay Lakhujani
17 months ago by
Vijay Lakhujani4.0k
India
Vijay Lakhujani4.0k wrote:

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

ADD COMMENTlink written 17 months ago by Vijay Lakhujani4.0k

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 17 months ago • written 17 months ago by majeedaasim30
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