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BLAST: find short complementary between two sequences

Hi Guys, I run into a simple biological question: using the sequence from a particular RNA to find any SHORT potential sequence complementarity of this RNA with other mRNAs in human. I would require probably at least 18nt. I guess the way to solve it is to use BLAST and compare sequence A with all mRNA database. However I don't know how to set parameters to allow short alignments results to show up. My RNA is about 1k long hence all mapping tend to give longer alignment results. I am planning to run BLAST command line and tune parameters a bit but I have no clue where to start. Can anyone have more experience with such strange BLAST requirement share some clue? Many thanks!

Cheers, Sunny

alignment blast
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written by QYSunny • QYSunny

To extend the list of reported HSPs to smaller ones, you need to reduce the window size and increase the expect threshold.

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written by Jean-Karim Heriche Jean-Karim Heriche

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