Question: Confirming predicted gene model by RNA-Seq data
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gravatar for thitrucminh.nguyen
10 weeks ago by
thitrucminh.nguyen0 wrote:

Dear Everyone,

I am just wondering if we have any available tool to automatically confirm that a predicted gene model is correct or not based on RNA-Seq data? The only way to examine a gene model that I know is to visually compare the gene model and the RNA-read coverage on GBrowse. However, this method is time-consuming. If I have thousands of proteins which are candidates to be selected for further cloning, expression and biochemically characterization steps, and I have RNA-Seq read data of the genes encoding these proteins, could you please tell me how I can quickly know which proteins have correct gene models? Any ideas from you will be much highly appreciated.

Kindly regards,

Minh Nguyen

rna-seq gene prediction • 182 views
ADD COMMENTlink modified 10 weeks ago by theobroma221.0k • written 10 weeks ago by thitrucminh.nguyen0

What kind of information (of the predicted models) that you have currently: genomic coordinates, protein sequence, or? Honestly I don't really get your point on what to confirm by RNA-seq, protein or gene model? It's a bit of a more complex task (it's another story), since protein levels are not necessarily correlating with (supposedly corresponding) RNA levels.

ADD REPLYlink written 10 weeks ago by aka001180

Thank you for your reply! I have protein and CDs sequences. I need to check if the corresponding predicted gene models of these protein/CDs sequences are correct or not. The RNA-Seq read data is used to check the gene models.

ADD REPLYlink written 10 weeks ago by thitrucminh.nguyen0

Use a BLASTP program, then TBLASTX to confirm with your RNAsequences.

ADD REPLYlink written 10 weeks ago by theobroma221.0k

Thanks for your suggestion!

ADD REPLYlink written 9 weeks ago by thitrucminh.nguyen0
0
gravatar for theobroma22
10 weeks ago by
theobroma221.0k
theobroma221.0k wrote:

You could take all your gene sequences and use your local NCBI Blastx program. In the command line, just note that you only want the top blast result.

ADD COMMENTlink written 10 weeks ago by theobroma221.0k

Thanks for your reply!

ADD REPLYlink written 9 weeks ago by thitrucminh.nguyen0

Can you upvote or confirm that either of these processes worked for you please.

ADD REPLYlink written 9 weeks ago by theobroma221.0k
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