primer designing

[shekar]

dear sir/madem

i am working in molecular biology lab ,i need to know designing primers for a specific gene, hole genome, please let me know the process , online sites & need hints,I have whole genome(DNA) sequence ,

thank you
shekar
8143438656

[durgaprasad]

please reed the pcr & primer designing basics

[testsubjectzz]

For designing primers I use SE Central Clone Manager, this tells me hairpins/dimers/runs/melting etc about the primer that I'm designing.

[magicsiew]

Go GenBank and search nucleotide for the gene/genome u are targeting. For whole genome, normally design ribosomal RNA will be very effective since they appear throughout the genome. For targeting specific gene, let say a transefase, you will need to find in the genbank for that specific gene sequence.

From the sequence u obtain from genbank. You can directly use ncbi primer design function to "pick" out the primers. Normally they will give many set of primers, analyse them to select the better one. Length should be about 19 to 30nt, CG% about 50%, low level of hairpin,dimer,loop formation, and Tm of about the same so that u can optimize the Ta more easier.

If the gene u are targeting us not annotated in genbank, you will need to search for as many as possible of the same gene of related species that u can find. From those sequences, do alignment and find the conserve regions to design the primers.

[wilsontrace]

dear sir/madem

i am working in molecular biology lab ,i need to know designing primers for a specific gene, hole genome, please let me know the process , online sites & need hints,I have whole genome(DNA) sequence ,

Hi,
With Array Designer from Premier Biosoft (www.premierbiosoft.com) you can design primers to detect every gene or exon in the whole genome. The program enables you to detect differentially and alternatively spliced transcripts, SNPs and DNA sequence variation.
Visit - http://www.premierbiosoft.com/dnamicroarray/index.html
Cheers
Wilson