Question: BLAST: find short complementary between two sequences
gravatar for QYSunny
10 days ago by
QYSunny0 wrote:

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

blast alignment • 107 views
ADD COMMENTlink written 10 days ago by QYSunny0

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

ADD REPLYlink written 9 days ago by Jean-Karim Heriche20k
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