premier sequence analysis software

Paul Morrison morrison at farber.harvard.edu
Sat Apr 25 07:59:57 EST 1998

Andy Law wrote:

> In article <6hj3d0$a8s at net.bio.net>, John Crock <jcrock at mail.wsu.edu> wrote:
>  >  Our Vax operated GCG package is being shut down at our Univeristy.  I am
>  >  in charge of finding a new sequence analysis package for our
>  >  Department.  I am interested in knowing what is considered the premier
>  >  package regardless of cost?  We want to be able to enter
>  >  ABI traces directly into the program and access them from various parts
>  >  of the package.  What are the genome people using?
>  >
>  >  Is GCG the best?
>  >  What about Intelligentics or DNAstar by lasergene?
>  >  Are there others?
>  >  Cost is not a factor
> What you need depends on what you intend to do. Are you building huge
> contigs, or sampling short ESTs and searching against the databases?
> Looking for polymorphisms by sequencing multiple alleles?
> I assume that you are assembling contigs by your ABI trace requirements.
> A bit more info will be helpful
> Andy Law
> ------------------
> ( Andy.Law at bbsrc.ac.uk )
> ( Big Nose in Edinburgh )

I would side with Andy here that this question gets asked about twice a year
but in order to answer the specifics of the problem have to be spelled out. But
that wont stop me.

I'm just going to list my favorite things GCG does and list the program that
would replace it.

Protein to Protein homology alignments: MegAlign/ DNAStar  Mac/PC
  This is one category that GCG has some unique twists that nothing else has
but MegAlign for the most part has the superior alignment of two or many
proteins. Take 6 proteins that PSI Blast has found and this will align them.
You always have to do a little pushing and shoving for the weak alignments. A
mouse/human alignment snaps in place. I wish MegAlign would work a little bit
more intuitively for the final tweak of the alignments but all in all it is the

DNA sequence Contig Building: Sequencher 3.0 /Gene Codes  Mac/ (and now!) PC
Although other programs are creeping up Sequencher is still the leader in
Contig building. It's the fastest (including all unix programs) most intuitive
program for aligning DNA sequence. Andy mentions huge contigs: not a problem,
polymorphisms: piece of cake. It identifies them and then click, the
chromatograms are stacked in front of you. With Big Dye terminator and a wild
type run the polymorphism jumps right out .  I site license this program and
hand it out to the institute. One of these days I'm going to give the "How to
use Sequencher" seminar but since it is so easy to use I've never had to do it.

Sequence editing: You may laugh but my favorite still is DNA Strider 1.2  Mac
Unchanged since 1992 but when someone writes good code it lasts. Runs fine on
the newest G3's. If Christian Marck would make the editing window sizable it
would be perfect. This program is still the best at making nice restriction
maps, ORF maps, find a hairpin and all the rest of those simple things. It
still comes closest to sequence into the journal tables.

Database Searching: An internet browser and NCBI, Baylor,  WashU or a bunch of
other web sites. The price is right and updating the database is someone else's

Dealing with 200,000 .seq files: BBEdit 4.5  Bare Bones Software Mac
I throw this one in as the program that fills a lot of weird gaps if you're not
on a computer that has GREP and a few other handy commands. BBEdit is a
stripped down text editor that can search through several thousand files for
that one motif or name or site or enzyme that you misplaced and list all the
hits all at once in a new window. It will look in code, data, or text if you
want. It's also a great HTML code editor but I'm getting off topic.

So that's my list of replacement parts for GCG. Since I pulled the plug on GCG
in '88 I _might_ be missing some of the improvements.

Hope this helps, Paul

Paul Morrison  D830
Molecular Biology Core Facilities
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115
p_morrison at dfci.harvard.edu
phone 617-632-3082
fax  617-632-4814

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