Confirming predicted gene model by RNA-Seq data

Question

[thitrucminh.nguyen]

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

[aka001]

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.

[thitrucminh.nguyen]

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.

[theobroma22]

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

[thitrucminh.nguyen]

Thanks for your suggestion!

Answer 1

[theobroma22]

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.

[thitrucminh.nguyen]

Thanks for your reply!

[theobroma22]

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