sequence programs

Eric C. Anderson anderson at pharmdec.wustl.edu
Sun Mar 19 14:23:42 EST 1995


In article <reedc-1303952101200001 at ip043167.iac.net>, reedc at iac.net
(Daniela Sciaky) wrote:

> We are in the need of purchasing sequence analysis programs for the
> Macintosh. We are familiar with MacVector and while it is OK it doesn't do
> the best job finding alignments.  Anybody have any opinions (I know you
> do) about what they like or dislike about various programs. I need your
> opinions soon. Thanks.

our lab has been using GeneWorks from Intelligenetics for about 3 years
now.  while i like that it has a lot of features and will do almost
anything that i've ever wanted it to do, it does them very slowly (even on
our Quadra 840AV) and very often does a weird job of making DNA and protein
alignments.

we've been using a demo version of a program called Sequencher from Gene
Codes.  it can handle chromatographs from our ABI 373 sequencer (which is
really nice when you're trying to reconcile discrepancies in contigs) and
it is FAST.  i recently raced them with a set of 8 sequences of about 400bp
going in both directions over a 1.5kb gene as well as the full gene
sequence itself (9 total sequences).  Gene Works took 50 seconds to do the
contig where Sequencher took only 7 seconds to do it.

the downside is that Sequencher really only does alignments and contigs (as
well as translations).  if you want to deal with protein sequences at all,
you will need another program.  the upside is that what it does it does
very well and very fast.  i don't have the info on the program in front of
me, but if you want  to get a demo version, let me know and i'll send you
the address of the company.

good luck,
eric
-- 
eric c. anderson                                
anderson at pharmdec.wustl.edu
dept. of molecular bio. and pharm.               (314)362-3963 (lab)
washington univ. school of medicine              (314)862-2435 (home)
660 s. euclid box 8103                           (314)362-7058 (FAX)
st. louis, mo 63110



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