BLAST: find short complementary between two sequences

Question

[QYSunny]

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

[Jean-Karim Heriche]

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