I have a unknown transcript and want to find out its CDS region translated into protein. Kindly help me which bioinformatics tools will be helpful in finding this information.
Hi Fizzah,
you should blast your sequence again the right species genome (choose "Refseq Genome Database") in one of the NCBI tools (https://blast.ncbi.nlm.nih.gov/Blast.cgi) and see what next.
fred
Hi,
I found BioEdit to be very helpful for this task. An oldie but goldie. Give it a shot.
http://www.mbio.ncsu.edu/BioEdit/bioedit.html
Best
I agree with Frederic
- Blast the sequence and then examine the full length transcript it maps to in Genbank
- That way it should be possible to find the CDS region that actually makes the protein
- If you are now sure how to do that find attached an SOP describing similar operations; you should have what you need in here
Laurence Stuart Dawkins-Hall I already have examine the transcript with Blast predicted sequence.. the CDS region it shows is obviously of the known gene..But my question is I want to find CDS in unknown transcript ...I want to find out CDS in unknown trancript.I hope you understand my question
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