Answers.Body: <p>For the first question: "how many of long non coding can make hairpin loop structure?"</p>
  
  <p>The easiest thing to would be to run your sequences through an RNA secondary structure prediction tool. There's a few tools for doing this but the most commonly used are <a href="http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi" rel="nofollow noreferrer">RNAfold</a> from the <a href="https://www.tbi.univie.ac.at/RNA/" rel="nofollow noreferrer">ViennaRNA package</a> and <a href="http://unafold.rna.albany.edu/?q=mfold" rel="nofollow noreferrer">mfold</a>. </p>
  
  <p>This will give you an output that looks like this, where the parentheses indicate which bases are paired with each other. </p>
  
  <p><code>
  GGGCUAUUAGCUCAGUUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGCUGAUUCGAAUUCAGCAUAGCCCA
  (((((((..((((.........)))).(((((.......))))).....(((((.......)))))))))))).
  </code></p>
  
  <p>To see if there's hairpins, you'll need to annotate the elements within it. Take a look at <a href="https://www.biostars.org/p/4300/" rel="nofollow noreferrer">this question on biostars</a> for an example of how to do this. In short, you can use the <a href="https://github.com/ViennaRNA/forgi" rel="nofollow noreferrer">forgi</a> library to produce an annotation like this:</p>
  
  <p><code>
  (((((((..((((.........)))).(((((.......))))).....(((((.......)))))))))))).
  sssssssmmsssshhhhhhhhhssssmssssshhhhhhhsssssmmmmmssssshhhhhhhsssssssssssse
  </code></p>
  
  <p>If there's an <code>h</code> in the output annotation, you have a hairpin. The remainder of your question about annotating miRNAs will be left to somebody else.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-06-29T23:48:35.127Z
Answers.Text: hairpins are quite easy to identify using the bracket notation; just look for brackets that are in a left-right orientation with nothing in between (e.g. `(.)`, `(..)`, `(...)`).
Answers.UserDisplayName: gringer
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Answers.CreationDate: 2017-06-29T19:20:15.247Z
Answers.LastActivityDate: 2017-06-29T19:20:15.247Z
Answers.UserDisplayName: juniper-
Body: <p>I have done de novo assembly of pair end raw read sequences and resulted transcripts sequences were separated based on coding potential into two categories: long non-coding RNA transcripts and coding RNA transcripts.</p>
  
  <p>I want to find how many of long non coding can make hairpin loop structure and how can I annotate these miRNA which are generated from long non coding RNA in plants.</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-29T09:08:53.207Z
Comments.Text: Welcome to Bioinformatics! Is there anything you tried before posting? Is there any reason why you tagged the question with Bioconductor (Maybe you want to restrict to use a Bioconductor package, or have used one and you can't manage to make it classify your lnRNA)? Also, I think there are two questions here: how to find if a lncRNA can make hairpins and annotate RNA to miRNA. It would be better to focus in just one question (perhaps the first one and later on the second one).
Comments.UserDisplayName: llrs
Tags: <bioconductor><rna-structure>
Title: How to find hairpin loop structure in a large set of long non coding RNA transcripts
ThreadText: # How to find hairpin loop structure in a large set of long non coding RNA transcripts
  
  (Asked by: username_0 on 2017-06-29)
  
  I have done de novo assembly of pair end raw read sequences and resulted transcripts sequences were separated based on coding potential into two categories: long non-coding RNA transcripts and coding RNA transcripts.
  
  I want to find how many of long non coding can make hairpin loop structure and how can I annotate these miRNA which are generated from long non coding RNA in plants.
  
  **Tags:** bioconductor, rna-structure
  
  > **Comments:**
  > **username_1**: Welcome to Bioinformatics! Is there anything you tried before posting? Is there any reason why you tagged the question with Bioconductor (Maybe you want to restrict to use a Bioconductor package, or have used one and you can't manage to make it classify your lnRNA)? Also, I think there are two questions here: how to find if a lncRNA can make hairpins and annotate RNA to miRNA. It would be better to focus in just one question (perhaps the first one and later on the second one).  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2017-06-29. Score: 4
  
  For the first question: "how many of long non coding can make hairpin loop structure?"
  
  The easiest thing to would be to run your sequences through an RNA secondary structure prediction tool. There's a few tools for doing this but the most commonly used are [RNAfold](http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi) from the [ViennaRNA package](https://www.tbi.univie.ac.at/RNA/) and [mfold](http://unafold.rna.albany.edu/?q=mfold).
  
  This will give you an output that looks like this, where the parentheses indicate which bases are paired with each other.
  
  `GGGCUAUUAGCUCAGUUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGCUGAUUCGAAUUCAGCAUAGCCCA
  (((((((..((((.........)))).(((((.......))))).....(((((.......)))))))))))).`
  
  To see if there's hairpins, you'll need to annotate the elements within it. Take a look at [this question on biostars](https://www.biostars.org/p/4300/) for an example of how to do this. In short, you can use the [forgi](https://github.com/ViennaRNA/forgi) library to produce an annotation like this:
  
  `(((((((..((((.........)))).(((((.......))))).....(((((.......)))))))))))).
  sssssssmmsssshhhhhhhhhssssmssssshhhhhhhsssssmmmmmssssshhhhhhhsssssssssssse`
  
  If there's an `h` in the output annotation, you have a hairpin. The remainder of your question about annotating miRNAs will be left to somebody else.
  
  > **Comments:**
  > **username_3**: hairpins are quite easy to identify using the bracket notation; just look for brackets that are in a left-right orientation with nothing in between (e.g. `(.)`, `(..)`, `(...)`).  
  
  ---
  
  