<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>

CC BY-SA 3.0
2017-06-29T23:48:35.127Z
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. `(.)`, `(..)`, `(...)`).
gringer
CC BY-SA 3.0
2017-06-29T19:20:15.247Z
2017-06-29T19:20:15.247Z
juniper-
<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>

CC BY-SA 3.0
2017-06-29T09:08:53.207Z
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).
llrs
<bioconductor><rna-structure>
How to find hairpin loop structure in a large set of long non coding RNA transcripts
# 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. `(.)`, `(..)`, `(...)`).  

---

