How to know the coding regions

[Waqasuddin Khan]

Hi,

I have four plant samples of RNA-Seq experiments, now in terms of unigenes (nucletoide fasta files). I want to know the coding regions that are present within these nucelotides sequences.

Any tools or webserver???, overall I have ~ two hundred thousand nucleotide sequences.

Thanks,

Waqas.

[GenoMax]

Are these assembled/analyzed or still raw reads ("unigene" means something specific: http://www.ncbi.nlm.nih.gov/unigene)?

If you know of a closely related plant genome you could setup local blastx searches with a protein database. If those 200,000 sequences are redundant then you may want to use "CD-HIT" to first cluster them before you do blast.

[colindaven]

cd-hit-est is effective. Then perhaps look at transdecoder http://transdecoder.github.io/
to predict ORFs. The BLASTx step might be necessary but will be computationally expensive.

[Waqasuddin Khan]

Thanks guys for great help,

Now, I am planning to cluster my sequences first, than try transdecoder for coding sequences. Perhaps, I will use Expasy's Translate tool (http://web.expasy.org/translate/) to convert nucleotide to protein sequences.