Hello,

I am looking at designing degenerate primers to detect between genotypes of viruses. I have to align around 1290 nucleotide sequences available in the genbank and then design primers based on the consensus seen.

Can anyone suggest me a program that will help me to do this.


the kid

Look up the following search results for online tools and choose any one.
Primer Design Programs
Degenerate Primer Design

Probably this is what you are looking for
PCR primers designed from protein multiple sequence alignments at http://blocks.fhcrc.org/blocks/codehop.html

Hi,

May I suggest you to have a look at AlleleID? AlleleID can design degenerate primers in the conserved region after identifying it using an alignment. This option is available in both the SYBR Green and TaqMan mode.

For details, please visit:
http://www.premierbiosoft.com/bacterial-id...tion/index.html

and request a key to use your own data if interested

Hope this helps.

Regards,
Fatema Sidhpurwala
PREMIER Biosoft International

Hello,

Thank you for the information. But I am looking for a software for aligning nearly 1000 nucleotide sequences and then designing the primers based on the alignment. So would like to know if this programme can do alignment for 1000 nucleotide sequences.

thekid

hey hi,
you can align your sequence here at this link :
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PA...K_LOC=align2seq


and then ,after checking your primer you should use the whole seq and paste it on this link and it will give you your wanted primer :
http://frodo.wi.mit.edu/

You should be able to do this in the latest version of Geneious Pro Geneious Home Page