Question: Confirming predicted gene model by RNA-Seq data
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gravatar for thitrucminh.nguyen
16 days 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 • 115 views
ADD COMMENTlink modified 16 days ago by theobroma22980 • written 16 days 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 16 days ago by aka001170

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 16 days ago by thitrucminh.nguyen0

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

ADD REPLYlink written 16 days ago by theobroma22980

Thanks for your suggestion!

ADD REPLYlink written 7 days ago by thitrucminh.nguyen0
0
gravatar for theobroma22
16 days ago by
theobroma22980
theobroma22980 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 16 days ago by theobroma22980

Thanks for your reply!

ADD REPLYlink written 7 days ago by thitrucminh.nguyen0

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

ADD REPLYlink written 7 days ago by theobroma22980
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