<p>Firstly, I would download some sort of editor that is built to handle nucleotide sequences. There are a handful out there, but APE is a fairly popular software designed for plasmid editing. It is much more efficient at searching for nucleotide strings as it can search for reverse complements and to a certain extent, mismatches. It's also free!</p>

<p><a href="http://biologylabs.utah.edu/jorgensen/wayned/ape/" rel="nofollow noreferrer">http://biologylabs.utah.edu/jorgensen/wayned/ape/</a></p>

<p>For your question, I'm not exactly sure what you are asking, but I would use the BLAST alignment tool to try to see similarity between your RNAi sequences and the target mRNA. You input fasta files and the program searches for any possible overlap between the two inputs. The higher the "max-score" the more likely the two strands (or subsections of strands) have high similarity. This program also considers the complement</p>

<p><a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&amp;PAGE_TYPE=BlastSearch&amp;LINK_LOC=blasthome" rel="nofollow noreferrer">https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&amp;PAGE_TYPE=BlastSearch&amp;LINK_LOC=blasthome</a></p>

<p>You can use the results from BLAST to annotate in APE using different colors which is extremely helpful. You can also use BLAST in the user interface of APE. </p>

<p>Also keep in mind RNAi's are not always effective, even though they are predicted to bind at a given location, that may not be a biological reality </p>

<p>Good luck! </p>

CC BY-SA 3.0
2017-06-27T21:11:07.147Z
2017-06-27T21:11:07.147Z
C. Caggiano
<p>How can I work out at which sites on the Drosophila melanogaster CG2316 mRNA the RNAi`s: </p>

<ul>
<li>12170/FBti0089992, </li>
<li>12168/FBtp0030589, </li>
<li>107343/FBtp0042163 and </li>
<li>41984/FBst0034349 </li>
</ul>

<p>(stock numbers/flybase ID) cleave? </p>

<p>I attempted to work this out myself some time ago but with limited success. I found the Fasta sequence of CG2316 and searched for the two complementary sites of the RNAi hairpin using the word doc find function. I feel this rudimentary method was flawed on a few levels, not least because I only got a single hit. As such I have posted the problem here.</p>

CC BY-SA 3.0
2017-08-05T11:02:17.220Z
From FlyBase, FBti indicates a transposable element insertion site. Searching for these in combination with your stock numbers gives nothing. Are these commercial RNAis? If so, how are we to know what their sequences are without further information?
David
<fasta><transcriptome-regulation>
Can you tell me where these RNAi’s cleave on the Drosophila melanogaster CG2316 mRNA?
# Can you tell me where these RNAi’s cleave on the Drosophila melanogaster CG2316 mRNA?

(Asked by: username_0 on 2017-06-16)

How can I work out at which sites on the Drosophila melanogaster CG2316 mRNA the RNAi`s:

* 12170/FBti0089992,
* 12168/FBtp0030589,
* 107343/FBtp0042163 and
* 41984/FBst0034349

(stock numbers/flybase ID) cleave?

I attempted to work this out myself some time ago but with limited success. I found the Fasta sequence of CG2316 and searched for the two complementary sites of the RNAi hairpin using the word doc find function. I feel this rudimentary method was flawed on a few levels, not least because I only got a single hit. As such I have posted the problem here.

**Tags:** fasta, transcriptome-regulation
> **Comments:**
> **username_1**: From FlyBase, FBti indicates a transposable element insertion site. Searching for these in combination with your stock numbers gives nothing. Are these commercial RNAis? If so, how are we to know what their sequences are without further information?  

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## 1 answers

### Answer by username_2 on 2017-06-27. Score: 1

Firstly, I would download some sort of editor that is built to handle nucleotide sequences. There are a handful out there, but APE is a fairly popular software designed for plasmid editing. It is much more efficient at searching for nucleotide strings as it can search for reverse complements and to a certain extent, mismatches. It's also free!

<http://biologylabs.utah.edu/jorgensen/wayned/ape/>

For your question, I'm not exactly sure what you are asking, but I would use the BLAST alignment tool to try to see similarity between your RNAi sequences and the target mRNA. You input fasta files and the program searches for any possible overlap between the two inputs. The higher the "max-score" the more likely the two strands (or subsections of strands) have high similarity. This program also considers the complement

<https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome>

You can use the results from BLAST to annotate in APE using different colors which is extremely helpful. You can also use BLAST in the user interface of APE.

Also keep in mind RNAi's are not always effective, even though they are predicted to bind at a given location, that may not be a biological reality

Good luck!


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