Sequence Alignment and Primer Design Softwares?

Erich Schwarz schwarze at starbase1.caltech.edu
Fri May 20 21:40:43 EST 1994

In article <2psafk$l1 at molbio.usc.edu>, zarow at molbio.usc.edu (Chris Zarow)

> I am seeking recommendations for some software programs. 
> 1.   A sequence alignment program for cDNAs.   The sequence alignment program
> should be able to align several sequences at once, and report on both 
> homologous and non-homologous regions across sequences. 

    Obtain MACAW from ncbi.nlm.nih.gov (they've got an ftp site that
accepts "anonymous" as a login and your e-mail address as a password. 
MACAW's fantastically good, and the documentation includes excellently
readable (albeit challenging) references in _Science_ and elsewhere.  It's
the best multi-sequence alignment program in the world that I know of, and
it's freeware.

> 2.   A primer-design program able to adhere to criteria for Tm, %GC, 
> lack of primer-dimers, lack of hairpin loops, etc.

    OSP, I believe, is used by the C. elegans sequencing consortium with
some luck.  I have not myself found primer-design programs helpful, but
that's a highly personal finding.  I don't know if OSP is freeware or not.

--Erich Schwarz / schwarze.ccomail at starbase1.caltech.edu

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