Question: How to find SSR location i.e whether it is in CDS, or UTR
gravatar for majeedaasim
17 months ago by
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?


location rna-seq ssr • 650 views
ADD COMMENTlink modified 17 months ago by Vijay Lakhujani4.0k • written 17 months ago by majeedaasim30
gravatar for Vijay Lakhujani
17 months ago by
Vijay Lakhujani4.0k
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.


ADD REPLYlink modified 17 months ago • written 17 months ago by majeedaasim30
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1017 users visited in the last hour