How to find SSR location i.e whether it is in CDS, or UTR
1
0
Entering edit mode
4.0 years ago
majeedaasim ▴ 60

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 • 1.5k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
4.0 years ago

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

ADD COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 1702 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6