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From: droufa@MATT.KSU.KSU.EDU (Donald J Roufa)
Newsgroups: bionet.molbio.genbank
Subject: Re: A question for FTP users
Message-ID: <9101241525.AA26205@matt.ksu.ksu.edu>
Date: 24 Jan 91 15:25:59 GMT
References: <9101232140.AA25920@genbank.bio.net>
Sender: daemon@genbank.bio.net
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Bruce Roe writes:
 
> 
> Give me a break.  How many many vendors is *every* ? Do folks really
> search the entire GenBank from their pc's?  Some search the protein
> databases on their pc's/macs but the entire GenBank?
> 
> Could we at least concentrate our discussion on MainFrame computer
> programs and databases on these.  Maybe I'm mistaken but I count
> three MainFrame program sets as the vast majority used, GCG, IG, and
> NBRF/PIR.  A few sites have the Staden programs but most of us who use
> the Staden programs use them for purposes other than database searching.
> 
> In reality, Bill Pearson's FASTA and companion programs probably are
> used the most and they handle the GCG formatted databases.
> 
> I think what we need here is a survey of what's out there.  If we limit
> our discussion to Main Frame programs and FTP sites and not deal with
> individual users but rather with sites. I also do not think we should
> consider other forms of the databases, such as those which require
> pre-processing for the NLM BLAST programs or GCG's QUICKSEARCH.
> 
> 
	Although I agree that users carrying out sophisticated
analyses of GenBank on PCs are severely handicapped by their machines'
command of memory and speed, as a 'bench' molecular biologist who
frequently uses GenBank information for experiments, I have found that
most of my searches are not sophisticated ones.  They simply are
requests to retrieve a single locus within the database, or, as Bruce
asserts, are TFASTA sequence comparisons.  The former are most
conveniently done on our laboratory PCs using the CD-ROM or floppy
report release.  The latter are best done, as suggested, on mainframes
or via e-mail directly to GenBank, but they can also be carried out in
just a few minutes (20 minutes to be precise) for TFASTA search on a
80386 PC.  Since the vast majority of working laboratories have access
to PC's, whereas only a subset of them have close ties to mainframes,
I think that Dr. Roe's suggestion would not be in the best interests
of the entire population of working molecular biologists.  In
addition, it has been my experience that, despite the fact that I do
use our university's mainframe and unix network for GenBank work, as a
research scientist I have little influence over our institution's
allocation of mainframe computing resources.  In contrast, I have
complete control over our local microcomputing resources, and can
tailor our database needs for research quite specifically at that
level.  Inasmuch as GenBank is, in fact, a research resource, it is
important that we not lose site of its use by people who are
depositing data in the database.

-- 
    Don Roufa        E-Mail: DROUFA@MATT.KSU.KSU.EDU    //  | /  /---  |  |
Division of Biology          DROUFA@KSUVM.KSU.EDU      //   |/   |__   |  |
Kansas State Univ.   Tel: (913) 532-6641              //    |\      |  |  |
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