Primer Design - aligning sequences for probe/primer design (Sep/05/2010 )

Hi Everyone,

Have got a question which I think might be quite obvious, but I'm not 100% sure as I am a newcomer to all this. Here it goes -->

I have downloaded a set of nucleotide sequences for a specific gene I'm interested in (FASTA format). Some of the sequences say "+ strand" and some say "- strand". It would seem obvious to me that before aligning the sequences to design my probe/primers, I would transform the + strand to its complement. I would just like to know if this is correct.

Thanks a lot!

a

-autoclave-

just use NCBI's primer design tool on its website and you don't need to confuse yourself. the forward primer binds to - strand, and reverse primer to + strand.

-Curtis-

yes, u can use primer3-blast on NCBI

Curtis on Mon Sep 6 08:15:28 2010 said:

just use NCBI's primer design tool on its website and you don't need to confuse yourself. the forward primer binds to - strand, and reverse primer to + strand.

-susanna-