BLAST of shRNA sequence
Posted 06 December 2011 - 10:32 AM
I want to blast my shrna sequence to see if it is specific. I used megablast (NCBI) and nucleotide collection as database. I got many many things other than my gene of interest.
Could you please tell me, how I can determine if my shrna is specific enough to my gene of interest? Is "total score" a good representative for specificity? Should I use nucleotide collection as database or refseq-rna (this one gives less hits)?
Posted 06 December 2011 - 05:09 PM
Posted 07 December 2011 - 02:38 PM
what is seed region? sorry I know it is a silly question....I got what I attached to this post. it is around 100 other genes that are matching my antisense sequence. does it mean this shrna has lots of off targets?