This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to find SSR location i.e whether it is in CDS, or UTR

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

rna-seq ssr location
• 3,239 views • link
updated by Abhishek • Abhishek • written by majeedaasim • majeedaasim

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

• 0 views • link
written by Abhishek • Abhishek

1 answer

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

• 0 views • link
written by lakhujanivijay lakhujanivijay

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

• 0 views • link
written by majeedaasim • majeedaasim

Log in to answer this question.

More posts like this