Tool for matching two complementary sequences - (Dec/29/2019 )

Dear All, 

H have two RNA sequences, and I am looking for a tool that allow me to obtain a score or value or at even a figure of how they are complementary to each other. This is quite of value in case I am looking whether piRNAs ( a small non-coding RNA) can target (be complementary to ) influenza genome ? Any help 

Hi,

I'm sure there are many ways to do this, but I can think of a few that I used for similar purposes.

The most obvious: you can submit your RNA to the Blast tool on the NCBI website- it should find the appropriate match if your influenza genome is in the database, and it should be.  You may have to use Oligo BLAST. If your RNA seq is a close match to multiple sites on the genome, the results will show this.

Do you have some kind of genetics software? You can use either assembly or alignment tools to align your RNA to its genome. It's a bit of a fudge method but works. I used to use Vector NTI.  Its Alignment tool tolerates mismatches, but expects the sequences to be about the same length, and in the same orientation. Therefore, you must enter the complimentary sequence in its reverse compliment form so it is the same as the other sequence.  To use the VNTI Assembly tool to match your sequences, they can be in different orientations to start, and different lengths, but the assumption is that there are no mismatches (except miscalled peaks where sequence quality is low), so very few mismatches are tolerated.  If you are trying to match a small RNAs to a large genome I think you could use the Assembly tool, even though you are not really "assembling." Neither of these methods will tell you if your RNA "hits" on your genome in more than one spot. 

I hope something here helps your specific goal.  I am recently retired so forgive me if there are newer options available.