Sequencher program for ABI373 data

Jason E Stewart jasons at bmc.uu.se
Fri Mar 12 15:17:00 EST 1993


In article <9303081431.AA28019 at geneman.wustl.edu>, rick at GENEMAN.WUSTL.EDU
(Rick Wilson) wrote:
> 
> 
> scarr at kean.ucs.mun.ca (Steve Carr) asks:
> 
> >I've just gotten the demo disk for the Sequencher program from Gene Codes.
> >It's looks reasonable, and so far as I am aware is the only program besides
> >ABI's own SeqEd that handles the chromatogram data from an ABI 373A.
> >
> >Before I shell out $1700, does anyone out there have extensive experience
> >with Sequencher, and how does it compare with SeqEd?
> 
> I can suggest two alternatives:  ted (Gleeson & Hillier, NAR 19, 6481) which
> runs on Sun SPARCstations and is available free from LaDeana Hillier (lfw@
> elegans.wustl.edu), and SeqMan from DNAstar which is not free (I don't know
> how much it costs) and runs on a Mac.  If you want to handle a lot of data
> and do sequence assembly and editing, I would strongly recommend ted as it
> has been integrated into the new Staden program xbap.  LaDeana can give you
> more information about that as well.

The recommendation of the Staden package is useful but only valid if you
have a connection to a SysAdmin who is going to mount the package on a UNIX
system and manage it for you, not to mention teach you the necessary X/UNIX
to be able to access the stuff, not to mention teaching anyone else who
wants to use the package (assuming that your purchasing this for a
department and not for solely personal use). This is a large time
investment. As more biologists take it upon themselves to learn UNIX, this
will pose less of a problem, but for someone who doesn't know UNIX the
learning curve for use the Staden package is very VERY low.

As far as DNAstar is concerned, their SeqMan package is a fairly well
thought out alignment program for shotgun sequencing projects, but not much
else. It is not a flexible program, nor is it very AEvent aware (i.e. no
publish/subscribe abilities), nor is there any way to save an alignment as
ascii to be incorporated into other programs. Another irritating part of
SeqMan is that you can't incorporate ascii text files into an alignment,
only ALF/ABI/EditSeq files can be incorporated. So any data you have
fetched up from a database (having used somehting other than their GeneMan
program) must be first converted to EditSeq format. DNAstar has just moved
another package to the Mac, MegAlign for doing other type of alignments as
well as parsimony analysis, but I haven't really had a lot of time to use
it, but I think it still leaves too many holes that need to be answered by
an all encompassing sequence editor. The other problem with DNAstar is
there overly anal protection scheme. We had endless amounts of trouble with
the two user version we purchased until we updated to a network version
(and now have little if no prolbems).

Getting over to SeqEd....

DON'T WASTE YOUR TIME!!!!! SeqEd is a dead end. It is not AEvent aware, all
the commands must be done manually (i.e. if you want to add 96 sequences to
an alignment you gotta do it 96 goddamn times). None of the useful commands
have keyboard equivalents (that is if you don't want to go in with
ResEdit). Even the "updated" version 1.0.3 has too many bugs that mean seq
file names get misread 1 time in 5. The Find/Replace command works only on
one seq at a time (i.e. you gotta do it 96 goddamn times - see adding
sequences above). You cannot have more than one alignment open at a time.
You cannot look at ALF files. ABI does not supply a printed version of the
manual. To change seq names you have to open a special window, which
increase the sheer number of keystrokes (see 96 goddamn times,above). I
could spend all day doing this.

I am still waiting for my Sequencher demo, but from all the messages I have
gotten from Howard Cash, I believe that it is by and far the best if not
the only all encompassing DNA seq alignment program on the market -
WARNING! I have not tested this product yet, and am relying on the info I
have gotten from other users as well as the companies owner H. Cash for my
info. I also believe that Gene Codes will be easier to deal with then
DNAstar as far as program modifications are concerned. However DNAstar was
stille pretty helpful and wuick about fixing bugs/incorporating changes. 

Trying to get ABI to make changes is about as teaching a pig to sing so I
have stopped trying.


----------------------------------------------------------------
Jason Stewart                                 Father at large
Department of Medical Genetics            jasons at bmc.uu.se
Biomedical Center, Box 589                Tel 46 18 17 49 10
751 23 Uppsala                            Fax 46 18 52 48 69
Sweden



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