How can we design a primer ? step by step method - (Mar/03/2012 )

Dear Members,

Can any one tell me step by step process of Primer Designing ...

not by software but using ncbi databases manually.

Please help me through this ...

What do you mean by "using ncbi database" ?
Do you mean using this: http://www.ncbi.nlm.nih.gov/tools/primer-blast/ ?


Have you checked this: http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html (its a general page on how to design primers)

Thanks Mr. Veteran,

The link that you had given about the primer design part was very useful.

and I have a doubt ... suppose if we need to design primers for a tetra arms pcr ...

then how to do ... i read some of the websites but couldnt get it .... can you please elaborate on this ...

thanks a lot for your support ...

check: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC55900/ and http://www.niab.com/uploads/files/Chiapparino_Genome04_tetra_ARMS_barley.pdf
and here you can start desinging primers:
http://cedar.genetics.soton.ac.uk/public_html/primer1.html and http://cedar.genetics.soton.ac.uk/public_html/primer1help.html#source_sequence

I cant really help you with this, I am not really familiar with tetra arms pcr.
Maybe you could also start a new post with tetra arms pcr as title (because some people might not read this topic because its about general primer design)

you can try out this program for tetra arms pcr:
http://cedar.genetics.soton.ac.uk/public_html/primer1.html

The software is described here