Question: RNA structure prediction-BLAST alignment to multiple sequence alignment
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gravatar for d.awwad19
24 months ago by
d.awwad190
d.awwad190 wrote:

Hi guys,

I know this might sound like a really basic question for some, but I'm a very beginner in bioinformatics and sequence analysis..

So, I ran blastn on NCBI-BLAST on an RNA sequence to which I intend to predict the secondary structure.. The output of the BLAST contains some sequences that are labeled "plus/plus" and some that are labeled "plus/minus"..

My question is: my next step should be multiple sequence alignment.. Should I flip the "minus" subject sequences so all the sequences in the MSA input are in the same orientation, or should I run MSA on the BLAST output sequences as they are?

Thanks in advance!

blast alignment • 763 views
ADD COMMENTlink modified 23 months ago by Biostar ♦♦ 20 • written 24 months ago by d.awwad190

The BLAST output should already be flipped. If you run RNA vs other RNA then you shouldn't expect plus/minus results, these results would only appear if your database is DNA.

ADD REPLYlink written 24 months ago by Asaf6.2k

It was actually the DNA exons sequence coding for the RNA molecule, but the ultimate goal is to predict the secondary structure of the RNA molecule. So as I explained in my question, some of the output sequences are in plus/minus format.. should I flip them so that all the sequences are in the same orientation before I run MSA?

ADD REPLYlink written 23 months ago by d.awwad190

If the input was the coding DNA then you shouldn't expect plus/minus results, unless you found a binding site for the RNA or something like that. I would take a second look in these results to see if they're valid. If most of your results are plus/plus (way over half which is expected at random) I would exclude the plus/minus. If you get about half plus/plus and half plus/minus recheck your dataset.

ADD REPLYlink written 23 months ago by Asaf6.2k
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