Answers.Body: <p>Is there any conserved secondary structure in this RNA? One could align all known instances of this RNA and see if there is any significant covariation according to <a href="http://eddylab.org/R-scape" rel="nofollow noreferrer">R-scape</a>. That could serve as a computational signal that the RNA is real (although wet lab experiments would still be needed).</p>
  <p>Another question is whether this RNA is already in <a href="https://rfam.org" rel="nofollow noreferrer">Rfam</a>? If so, then the job of making an alignment of known instances is easier.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-30T11:21:09.763Z
Answers.LastActivityDate: 2020-11-30T11:21:09.763Z
Answers.UserDisplayName: apetrov
Body: <p>I'm working with a set of homologous genes (let's call it gene A) from several bacterial species.</p>
  <p>I know (from previously published research) that in gene B (a close paralogue of gene A), there is a non-coding, antisense RNA. This antisense RNA regulates gene B by forming a duplex with the gene B mRNA.</p>
  <p>I have noticed that, sometimes, an antisense RNA would be predicted for gene A in the same location in the IMG/MER database. This is not predicted for all of the available gene A sequences, only some of them. IMG/MER uses INFERNAL to predict RNAs, I think.</p>
  <p>My question is - is there any way to assess how real this is without wet lab data? As it is, it could be that there's no actual antisense RNA in gene A, and this is a spurious prediction due to homology. Or it could be that the antisense RNA is present in all of the gene A sequences, and the RNA prediction software simply missed some of them. Is there a computational way of testing which of these options (if any) is more likely? Thank you for your time!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-25T17:31:09.887Z
Comments.Text: https://pubmed.ncbi.nlm.nih.gov/17631615/
Comments.UserDisplayName: Chris_Rands
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-26T11:45:32.793Z
Comments.Text: @Chris_Rands I don't think that software would work for my current problem (even if it wasn't abandonware)... It seems to distinguish between 'coding' and 'non-coding', which it doesn't feel like it'd help when the antisense RNA is inside the gene (so, it is coding in one frame by default). Thank you for trying though!
Comments.UserDisplayName: Laura
Tags: <rna><software-recommendation><non-coding>
Title: Is is possible to predict ncRNAs from sequence and homology alone?
ThreadText: # Is is possible to predict ncRNAs from sequence and homology alone?
  
  (Asked by: username_0 on 2020-11-25)
  
  I'm working with a set of homologous genes (let's call it gene A) from several bacterial species.
  
  I know (from previously published research) that in gene B (a close paralogue of gene A), there is a non-coding, antisense RNA. This antisense RNA regulates gene B by forming a duplex with the gene B mRNA.
  
  I have noticed that, sometimes, an antisense RNA would be predicted for gene A in the same location in the IMG/MER database. This is not predicted for all of the available gene A sequences, only some of them. IMG/MER uses INFERNAL to predict RNAs, I think.
  
  My question is - is there any way to assess how real this is without wet lab data? As it is, it could be that there's no actual antisense RNA in gene A, and this is a spurious prediction due to homology. Or it could be that the antisense RNA is present in all of the gene A sequences, and the RNA prediction software simply missed some of them. Is there a computational way of testing which of these options (if any) is more likely? Thank you for your time!
  
  **Tags:** rna, software-recommendation, non-coding
  
  > **Comments:**
  > **username_1**: https://pubmed.ncbi.nlm.nih.gov/17631615/  
  > **username_0**: @username_1 I don't think that software would work for my current problem (even if it wasn't abandonware)... It seems to distinguish between 'coding' and 'non-coding', which it doesn't feel like it'd help when the antisense RNA is inside the gene (so, it is coding in one frame by default). Thank you for trying though!  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-11-30. Score: 1 | Accepted answer
  
  Is there any conserved secondary structure in this RNA? One could align all known instances of this RNA and see if there is any significant covariation according to [R-scape](http://eddylab.org/R-scape). That could serve as a computational signal that the RNA is real (although wet lab experiments would still be needed).
  
  Another question is whether this RNA is already in [Rfam](https://rfam.org)? If so, then the job of making an alignment of known instances is easier.
  
  
  ---
  
  