BATCH PRIMER DESIGN SOFTWARE

[Andrea Hansen]

Hi

> Dear colleague,
> I'd be interested in a program allowing design of primers from multiple
> sequence alignments. I work on a virus which has several genotypes and
> subtypes. Generally, I perform a multiple alignment of several genomes
> corresponding to different types and subtypes (with Clustal for example, I'm
> working on PC) and I try to find manually what could be the best consensus
> to be introduced in the primer design program which can only work with a
> unique sequence.

You can find the program CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide
Primers) here:
http://blocks.fhcrc.org/blocks/codehop.html
It is exactly what you are looking for.

Other links for primer design are in my webcatalog at:
http://www.bioinformatik.de/cgi-bin/browse/Catalog/PCR/Primer_Design

Andrea

--
Andrea Hansen
Institut fuer Genetik    Tel   : ++49-531-391-5783
TU Braunschweig          Fax   : ++49-531-391-5765
Spielmannstr. 7          email : webmaster at bioinformatik.de
38106 Braunschweig       http://www.bioinformatik.de