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