sequence analysis software

Bruce Roe broe at aardvark.ucs.uoknor.edu
Fri Jun 19 08:23:00 EST 1992

In article <18JUN199210443325 at seqvax.caltech.edu>, mathog at seqvax.caltech.edu (David Mathog) writes...

Here's my $0.02 worth describing what we have:

1.  GCG, Staden, Phylip, ClustalV, Blast and other programs on a University
    owned/maintained/supported VAX 6250.  FREE (university policy is
    NO charges for computer usage) and I maintain this facility, which
    is used by over 120 users throughout Oklahoma, as a hobby, but we
    have a small grant from the state (approx $50k for software updates,
    VMS programming, user support, sect. help for documentation, etc
    for this state-wide centralized core facility).
2.  Two ABI 373A's in my lab and the data is transfered to a Sun
    SPARCStation (via NFS Share) where we do ALL the proof-reading and 
    contig assembly with the MRC/Wash.U. TED and XDAP programs.
    Also have a Sun IPX so two can access the SPARCStation server
    simultaniously.  I'm also the system manager for these UNIX boxes 
    (with a lot of help from friends in Physics and in the Engineering College).
3.  10 Mac's available in lab & office for students/postdocs/etc.  All
    are on an AppleTalk network connected to the campus ether-net via
    a Kinetics FastPath box.  The Mac's are used for typical Mac applications
    and to access the VAX for data analysis via VersaTermPro.  Three of
    the Mac's are IIcx's with ether-net cards and also can access the
    Sun's via MacX (but it's noticably slower than using the Sun's directly).
4.  Almost ALL of our sequencing is Taq-cycle-sequencing with reactions done
    in a PE/Cetus 9600 on Biomek robotic isolated single-stranded m13-based
    templates and we collect approx. 40,000 bases/day running the 2 ABI's
    twice a day. The clones are generated by physical shearing methods,
    sonication, nebulizer, french press and in some instances we sequence
    off double stranded templates with both forward and reverse fluor-labeled
    primers, or single-stranded templates with ABI-dye-terminators for gap
    closure.  (we are sequencing the human c-abl and bcr genes on chrom.
    9 and 22, respectively and have a grant pending to sequence large regions
    of human chromosome 22).
5.  If anyone wants more details, drop me a note and I'll send off a copy
    of our recent paper:

    S.L. Chissoe, Y.F. Wang, S.W. Clifton, N. Ma, H.J. Sun, J.S. Lobsinger,
    S.M. Kenton, J. D. White and B. A. Roe. Strategies for Rapid and Accurate
    DNA Sequencing. Methods: A Companion to Methods In Enzymology. 3, 55-65

6.  Other comments:

	a. Fluorescent sequencing, in our hands, is MORE ACCURATE than
		radio-labeled sequencing and if we NEVER run another
		radio-labeled sequencing gel I'll be forever happy.
	b. Our Mac/Sun/VAX environment works (DOS-based computers
		are only used as front-ends to the Biomeks and not
		for anything else)
	c. We really like the MRC/Wash.U. TED and XDAP programs and
		feel they are superior to anything else available,
		and they are available for much less $$ than other similar
	d. Without the VAX and the 120+ state-wide users, I'd go to
		GCG, Staden, etc on the SPARCStation exclusively but
		the VAX is there, it's free, and the SPARCStation requires
		the users to be a little more computer literate so we have
		not gone that route, except for a few senior people in my
	e. I agree completely with Dave's comments except to add that
		his "slave labor" in my case also includes a full-professor,
		namely me, ...............sigh.  
		I also see a trend in the more enlightened study sections
		NOW to allow programmer/system support costs if they are
		WELL JUSTIFIED.  These line item cuts usually are by our
		less enlightened (??) peers during the review process, NOT
		by the "granting agency".

Cheers to one an all and sorry that my $0.02 worth was longer than anticipated.
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--------- included Dave's message below  -----------
>1.  If you're setting up any kind of sequence analysis center keep in 
>    mind that the hardware costs are usually negligible compared to the labor 
>    costs.  The only time when this is not true is when system management 
>    is by slave labor (ie, grad students).  Personally, I think that 
>    the various granting agencies, and certainly the universities should
>    outright forbid that practice, but I'm not holding my breath.
>2.  Software costs can be pretty misleading.  "Single seat" 
>    software (like on a PC or Mac) is usually very expensive when you 
>    do any sort of cost/user analysis.  For this reason, GCG is a great
>    bargain at 3000/year (especially with > 100 users) compared to the PC
>    and Mac options.  This also shows up in service contracts and the like 
>    - it's cheaper to maintain a couple of Vaxes or Unix boxes than an army
>    of PCs. 
>    "Free" software is not without costs - maintenance on this stuff can be
>    quite a pain or a breeze, depending entirely on the whims of the 
>    program's author.  Sometimes you can get bugs fixed and documentation,
>    other times, no.
>3.  One system manager usually costs less than N "part time" computer
>    honchos distributed at one/lab.  However, there is a strong tendency to
>    budget for the latter and not the former.  There is an even stronger
>    tendency (apparently among granting agencies) to approve money for 
>    hardware but not for labor.  On this last point I'd like some feedback:
>    it's been reported to me that this gets lined out on grants, but I've
>    no personal experience with it.
>David Mathog
>mathog at seqvax.caltech.edu
>manager, sequence analysis facility, biology division, Caltech

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