Eternam pmaillar at
Thu Sep 16 03:44:25 EST 1999

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.
With the arbitrary chosen "consensus" sequence, I try to find "universal"
primers allowing amplification of all the types of the virus.
My interest would be a program able to find best primer pairs (even
degenerated) among the aligned sequences.
Do you think your program would be useful for this purpose because I do not
know any soft able to do this at that time.
Best regards

P. Maillard
Institut Pasteur.
pmaillar at

Arun Apte <arun.apte at> a écrit dans le message :
37DFF374.7607FF46 at
> I'm currently writing a batch primer design program that can design
> primers for 1000's of sequences at a time.  If such a program would be
> useful to you, drop me an e-mail describing the type of research you are
> doing and your primer design needs.  I will ask you a few questions to
> ensure the program will meet your needs and then send you an advanced
> copy of the program.
> Thanks,
> Arun Apte

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