HDTenEightyP/NetNews huggingface dataset:
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Newsgroups: bit.listserv.info-gcg
Date:         Wed, 16 Dec 1992 22:21:22 -0600
Reply-To:     Maggie <smith@GCG.COM>
              <INFO-GCG@UTORONTO.BITNET>
From:         Maggie <smith@GCG.COM>
Subject:      RE: New Genbank (NCBI) database
Comments: To:

The previous message that dealt with the elimination of the Organelle
section and addition of the EST section in GenBank was incomplete and
incorrect.  We apologize for any inconvenience it may have caused.

Please note that this does not affect you unless you receive GenBank
directly from NCBI and reformat it for use with the GCG software.


There was a typo in the instructions for the Organelle.Farm file.
We had:

ORGANELLE.FARM

    1) Edit the file genbank.farm to remove the line
                     ^^^^^^^
         gb_or

It should be:

ORGANELLE.FARM

    1) Edit the file organelle.farm to remove the line

         gb_or

The GCGUserSpecs file corrections are different for VMS and Unix.  Here are
the two versions:

GCGUSERSPECS.COM (VMS)

     1) Edit the file GenCom:GCGUserSpecs.Com to remove the line

          $ Assign/NoLog GenBankDir:Gb_Or                   Gb_Or

     2) Add the lines (if it is not already present)

           $ Assign/Nolog GenBankDir:Gb_EST                 Gb_EST
           $ Assign/NoLog "@GenRunData:EST.Farm"            EST


GCGUSERSPECS (Unix)

     1) Edit the file GenScript:gcguserspecs to remove the line

           name -q -s Gb_Or     GenBankDir:gb_or

     2) Add the lines

           name -q -s EST       "@GenRunData:est.farm"
           name -q -s Gb_EST    genbankdir:gb_est


Maggie Smith
Michael Hogan
help@gcg.com
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Newsgroups: bit.listserv.info-gcg
Date:         Wed, 16 Dec 1992 15:40:15 -0500
Reply-To:     Foteos Macrides <MACRIDES@WFEB2.BITNET>
              <INFO-GCG@UTORONTO.BITNET>
From:         Foteos Macrides <MACRIDES@WFEB2.BITNET>
Subject:      Re: New PIR format to GCG
Comments: To: info-gcg@utoronto.bitnet

In article <01GS5EPGOU6600007S@SCI.WFEB.EDU>, Martti Tolvanen <tolvanen@KLAAVA.H
   ELSINKI.FI> writes:
> A couple of weeks back I asked a question about using sequencs fetched
> from the PIR server (fileserv@nbrf.georgetown.edu).  The problem was
> that the format is no longer the old PIR format that FROMPIR recognizes.
>[...]

        The format is CODATA.  I have a VMS Fortran FROMCODATA which Don Katz
sent me a few years ago.  It still works with the current version of GCG for
VMS.  I assume it's OK for me to pass it on to anyone who requests it from me
and has a license for GCG.

                                Fote

=========================================================================
 Foteos Macrides           Worcester Foundation for Experimental Biology
 MACRIDES@SCI.WFEB.EDU     222 Maple Avenue, Shrewsbury, MA 01545
=========================================================================
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU
Subject: (no subject given)
Newsgroups: bit.listserv.info-gcg
Date:         Tue, 15 Dec 1992 17:12:48 HST
Reply-To:     Craig Moyer <CMOYER@UHUNIX.BITNET>
              <INFO-GCG@UTORONTO.BITNET>
From:         Craig Moyer <CMOYER@UHUNIX.BITNET>
Comments: To: INFO-GCG@utoronto.bitnet

unsubscribe  GCG-INFO  Craig L. Moyer
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Newsgroups: bit.listserv.info-gcg
Date:         Mon, 14 Dec 1992 13:57:38 -0400
Reply-To:     John Edward Hill 263-7689 <HILL@NYU-MEDICAL.MED.NYU.EDU>
              <INFO-GCG@UTORONTO.BITNET>
From:         John Edward Hill 263-7689 <HILL@NYU-MEDICAL.MED.NYU.EDU>
Subject:      RE: GCG for Unix/SunOS

Hi, Jimmy.  I just saw your question.  GCG's phone number is
608-231-5200.  They are also reachable via email: help@gcg.com

Ciao,
John
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU
From: zxmkr08@studserv.zdv.uni-tuebingen.de (Cornelius Krasel)
Subject: Bug in FASTA?
Organization: Comp. Center (ZDV) U of Tuebingen, FRG
Date: Fri, 18 Dec 1992 11:40:42 GMT

I stumbled across a possible bug in the FASTA software of the latest
GCG release.

I searched the GENBANK for possible homologies to the following oligo-
nucleotide:

Ak10.Seq  Length: 17  December 14, 1992  11:37  Type: N  Check: 810  ..
 
       1  TGGCAGGTTA TCAGGAA
 
This oligo has been designed to match genbank:ecoompt1 with two
mismatches. Surprisingly, ecoompt1 didn't show up in the 40 sequences
with the best score. So I fetched genbank:ecoompt1 and ran a fasta
between the two sequences. The homology wasn't found either but a
much worse one.
wordsearch was able to find the homology, BTW.

Could somebody out there enlighten me?

Cornelius.
--
/* Cornelius Krasel, Department of Physiological Chemistry, U Tuebingen    */ 
/* email: krasel@studserv.zdv.uni-tuebingen.de (Internet)   HAS CHANGED!!  */
/*        NO WIN/X400 MAIL POSSIBLE AT THE MOMENT!                         */
/* "People are DNA's way of making more DNA." (R. Dawkins / anonymous)     */
Newsgroups: bit.listserv.info-gcg
From: m-jk8594@GRANNY.CS.NYU.EDU (James Kyriannis)
Subject: GCG for Unix/SunOS
Organization: Courant Institute, New York University
Date: Mon, 14 Dec 1992 05:19:58 GMT

I've recently become a system administrator to a research facility running
SunOS, and we're interested in setting up Unix GCG.  Can someone
e-mail me an e-mail address or a phone number of someone I can contact
to get more information on GCG?

Thanks,

Jimmy Kyriannis
jimmy@wombat.phri.nyu.edu
(I'm using another account to get this message out onto USENET since news
 isn't running correctly at phri.edu)


---------------
Jimmy Kyriannis

UNIX System and Network Administrator
The Public Health Research Institute
455 First Avenue, Room #1074
New York, New York 10016

Telephone: 212-578-0822
Internet mail: jimmy@wombat.phri.nyu.edu

Newsgroups: bit.listserv.info-gcg
From: gwilliam@crc.ac.uk (Gary Williams x3294)
Subject: New Genbank (NCBI) database
Keywords: NCBI Genbank EST
Organization: MRC Human Genome Resource Centre
Date: Mon, 14 Dec 1992 09:33:58 GMT


Would GCG like to post on the INFO-GCG news-group/mailing-list
instructions for changes that are required for setting up the new
organisation of NCBI's Genbank 74.0 (released last with the 'organelle'
division removed and a new 'est' division added). 

They may also like to comment on the extremely short notice that NCBI
has given for these changes.  This strikes me as being rather
insensitive to the needs of the database users and a poor start to their
stewardship of this data. 

 
Gary Williams
 
Computing Services Section,            Janet:       G.Williams@UK.AC.CRC
MRC-CRC & Human Genome Mapping Centre, Internet:    G.Williams@CRC.AC.UK
Watford Rd, HARROW, Middx, HA1 3UJ, UK 
Tel 081-869 3294   Fax 081-423 1275    
 

-- 
GARY WILLIAMS,  Computing Services Section,  Janet:       G.Williams@UK.AC.CRC
MRC-CRC & Human Genome Mapping Centre,       Internet:    G.Williams@CRC.AC.UK
Watford Rd, HARROW, Middx, HA1 3UJ, UK
Tel 081-869 3294   Fax 081-423 1275   
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Newsgroups: bit.listserv.info-gcg
Date:         Fri, 18 Dec 1992 14:40:56 -0500
Reply-To:     victoria@HELIX.NIH.GOV
              <INFO-GCG@UTORONTO.BITNET>
From:         victoria@HELIX.NIH.GOV
Subject:      Re: Bug in FASTA?
Comments: To: Cornelius Krasel <zxmkr08@STUDSERV.ZDV.UNI-TUEBINGEN.DE>
Comments: cc: INFO-GCG%UTORONTO.BITNET@VTVM2.CC.VT.EDU

>I stumbled across a possible bug in the FASTA software of the latest
>GCG release.
>
>I searched the GENBANK for possible homologies to the following oligo-
>nucleotide:
>
>Ak10.Seq  Length: 17  December 14, 1992  11:37  Type: N  Check: 810  ..
>
>       1  TGGCAGGTTA TCAGGAA
>
>This oligo has been designed to match genbank:ecoompt1 with two
>mismatches. Surprisingly, ecoompt1 didn't show up in the 40 sequences...

You should be running FIND/BATCH/MISMATCH=2 to pick this up. Probably you
will want to run this as a batch job because it might take awhile and the
file it produces could be pretty large if you run it against ALL of
Genbank. I ran FIND/BATCH/MISMATCH=2 with your oligo against gb_ba:*
(bacterial section only of Genbank) on a VAX 4000/500 and obtained the
following results:

     Total finds:          8        (One of the finds was the desired
    Total length: 15,257,363             genbank:ecoompt1)
 Total sequences:      8,629
        CPU time:   01:24.56

I don't know enough about the FASTA algorithm to explain why it doesn't
pick up what you were looking for - but I DO know that FIND works well for
this type of pattern search.


E. Victoria Porter, Ph.D.          o    o
NIH/NIDR/SSS                     `-\-'`-/-'     When all else fails,
Bldg 30 - Room B28                 />  <\       there's always dancing!
Bethesda, MD  20892-0030          ~ ~  ~ ~
301-496-1621 / FAX:301-402-0667
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU
Full-Name: Michael Lonetto
Mailer: Elm [revision: 66.25]
Newsgroups: bit.listserv.info-gcg
Date:         Fri, 11 Dec 1992 12:03:38 CST
Reply-To:     lonetto@CALSHP.CALS.WISC.EDU
              <INFO-GCG@UTORONTO.BITNET>
From:         lonetto@CALSHP.CALS.WISC.EDU
Subject:      Re: Your removal from the INFO-GCG list
Comments: To: INFO-GCG-Request@UTORONTO.BitNet
Comments: cc: SYSJOHN@UTOROCI1.BitNet
              92 10:17 am

Hi,

Why have I been removed?  Is there some requirement for posting?  I have
participated in several discussions from the list, though I generally
respond via direct email to the person initiating the discussion.  I do find
the group of use and would prefer that I not be removed.

Sincerely,
Michael Lonetto

>
> Dear subscriber,
>
>   As of  Friday, December  the 11th  of 1992,  you have  been removed  from
 the
> INFO-GCG  distribution list  (INFO-GCG:  GCG Genetics  Software Discussion)
  by
> "\"John F. Cargill\"" <SYSJOHN@UTOROCI1.BITNET>.
>
> Virtually,
>
>    The LISTSERV management
>


--
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Michael Lonetto           608-262-4828/4620                  *************
University of Wisconsin         ****************                     ********
Dept. of Bacteriology               lonetto@psl.wisc.edu                    *
1550 Linden Dr.                           ********************
Madison, WI 53706                               lonetto@calshp.cals.wisc.edu
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU
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Newsgroups: bit.listserv.info-gcg
Date:         Fri, 18 Dec 1992 15:14:37 EST
Reply-To:     "Paul Keenan,
              Library Database Administrator" <keenan@HAL.HAHNEMANN.EDU>
              <INFO-GCG@UTORONTO.BITNET>
From:         "Paul Keenan,
              Library Database Administrator" <keenan@HAL.HAHNEMANN.EDU>
Subject:      Using a laserjetII with a postscript cartridge
Comments: To: info-gcg@utoronto.bitnet

One of our users would like to know if she can use her HP LaserjetII for
graphics output from GCG if she equips it with a Postscript cartridge.  She
would then just set up output for EPSF format and use the /pass parameter when
she executes the programs.  She has 2MB of memory on her printer.  I belive
this should work, but I don't have any experience with LaserjetIIs with
Postscript.  Does anyone have a similar setup?  If it works at all, how decent
is the output?

Also, I've heard a rumor of software that will allow you to print HPGL graphics
on a LaserjetIII with only 2MB of memory.  Does anyone know the name of this
and where I might find it?

Thanks in advance for any help you can give me.

Paul


================================================================================

H  H U  U   |Paul Keenan, Database Administrator   |Voice: 215-762-3270
HHHH U  U   |Hahnemann University Library M.S.449  |FAX:   215-762-8180
H  H UUUU   |Broad & Vine Phila., PA 19102         |Keenan@Hal.hahnemann.edu

================================================================================
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU
Newsgroups: bit.listserv.candle-l
Date:         Wed, 16 Dec 1992 09:15:15 EST
From:         Steve Greenfield <FEATS@VTVM1.BITNET>
Subject:      CL/GateWay and Security on MVS

We now run CL/GateWay Version 115 and I have Version 146 in-house from which
I can install.  We use ACF2 security on our MVS system for authorization of
resources.  One of our new development groups is designing a new students-
system for registration which will be client-server based (I may use some
erroneous terms because I'm new to this client-server arena).  As I under-
stand things, a student will access the IMS system (the server) from a work-
station which is connected to an TCP/IP network (the client).

Because of the inherent lack of security of this setup, we would like to
install MIT's 'Kerberos' authentication security system on an UNIX server.
The student can logon to a Kerberized client and receive a ticket from the
UNIX authentication server which can subsequently be used to request network
services to access the MVS/IMS registration server.

This is my simplistic view of how things might work.  For this to function,
I would imagine that the CL/GateWay, which is the front-end to our mainframe
access, would need to interface with the Kerberos system.  It may need to
interpret tickets sent from the student-client which were created during the
Kerberos authentication process.

Assuming my outline is even close to being accurate, does anyone know if
the CL/GateWay can function in this environment or if anyone has a GateWay
exit that interfaces with the Kerberos system?  If anyone has anything
resembling this set-up can you give me a holler to discuss these topics?



Stephen L. Greenfield                     Bitnet:   FEATS@VTVM1
Virginia Polytechnic Institute   ,/\      Internet: feats@vtvm1.cc.vt.edu
Blacksburg, Virginia           ,/   `\/`'\
                           ,/\/          /
                         ,/             <_          ._.
                        /                 `\       / /
             ,/\_     _/'                   `-`-\  |/
          ,/'    `_'_'  *  Blacksburg          \_> '
       ,/'                                    \__>_/\
      +----------------------------------------------+
Newsgroups: bit.listserv.xedit-l,comp.lang.rexx,comp.unix.questions
From: bvaughan@sheps.Princeton.EDU (Barbara Vaughan)
Subject: Re: XEDIT and REXX for UNIX
Originator: news@nimaster
Organization: Princeton University
Distribution: na
Date: Wed, 16 Dec 1992 18:35:16 GMT

In article <BzBIwA.F4y@news.udel.edu> pesek@brahms.udel.edu (John Pesek) writes:
>I apologize if this is an FAQ on any of the lists.
>I am interested in any versions of REXX and/or XEDIT for Unix (SunOS 4.1.2)
>either freeware, shareware or commercial.  Please reply to me privately.

This is becoming an FAQ.  This is the second such query in a few days. 
I've sent e-mail as requested, but am also posting the answer to forestall
more queries:

Assuming you mean the CMS XEDIT, there is a commercial product called
UniXedit, which I believe comes with REXX, available from the Dynasoft
Workstation Group. (800)228-0255 or (708)696-4450.  I've never used it, so
can't answer any questions.

Barbara Vaughan

Newsgroups: bit.listserv.xedit-l,comp.lang.rexx,comp.unix.questions
From: pesek@brahms.udel.edu (John Pesek)
Subject: XEDIT and REXX for UNIX
Organization: University of Delaware
Distribution: na
Date: Tue, 15 Dec 1992 20:43:21 GMT

I apologize if this is an FAQ on any of the lists.
I am interested in any versions of REXX and/or XEDIT for Unix (SunOS 4.1.2)
either freeware, shareware or commercial.  Please reply to me privately.
I will summarize for the lists if appropriate.

Thanks in advance,

John Pesek
pesek@brahms.udel.edu


Newsgroups: bit.listserv.xedit-l
From: MCMASTER@LSTC2VM.stortek.com (Jim McMaster)
Subject: Re: Deletes at bottom of screen leaves unexpected blanks
Organization: StorageTek SW Engineering
Date: Fri, 11 Dec 1992 19:39:08 GMT

In article <92345.101010KLASSEN@UVVM>
KLASSEN@UVVM.BITNET (Melvin Klassen) writes:
 
>BMahoney@LMSC.Lockheed.COM <6381710@LMSC5.IS.LMSC.LOCKHEED.COM> writes:
>>When I am editing a line at the bottom of the screen and that line 'wraps' so
>>that I cannot see more than the first 79 chars, as I use the Delete key the
>>characters to the right of my delete activity creep left toward my cursor as
>>the 'delete' eats up characters. Those characters that are wrapped and are not
>>on my screen when I start deleting do not creep back onto the screen at this
>>time and trailing blanks appear at the right end of the screen line. Okay- I
>>would simply expect to see the trailing characters that are off the screen
>>rejoin the text that I'm viewing when I press Enter or do some scrolling. But
>>in fact, when the wrapped line is redisplayed the rightmost characters stay
>>where they are and those blanks I saw on the screen are now actual spaces in
>>the text!!!!
>
>Since you must have used the 'SET VERIFY nn1 nn2' command to display only
>part of the logical record, XEDIT, by design(!), will only update those columns
>which you see on the screen.  If you use 'SET VERIFY 1 *', then XEDIT will
>wrap the logical line onto more than one physical line on your display,
>and the DELETE key does(!!!) cause text from the later physical lines to be
>pulled onto the first physical line, i.e., WYSIWYG editing.
 
This works for all but the last line on the screen.  If you "V 1 *",
and XEDIT cannot fit all of the last record on the screen, it displays
the amount that fits.  The DELETE key and ERASE EOF only affect the
portion on the screen, not the undisplayed portion.
 
Jim McMaster
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU
X-Mailer: ELM [version 2.3 PL11]
Newsgroups: bit.listserv.xedit-l
Date:         Wed, 16 Dec 1992 21:53:57 EST
From:         Scott Ophof <ophof@SERVER.UWINDSOR.CA>
Subject:      Re: XEDIT and REXX for UNIX
Comments: To: XEDIT-L@uga.cc.uga.edu
              at Dec 16, 92 6:35 pm

Barbara Vaughan said:
>In article <BzBIwA.F4y@news.udel.edu> pesek@brahms.udel.edu (John Pesek)
>writes:
>...
>Assuming you mean the CMS XEDIT, there is a commercial product called
>UniXedit, which I believe comes with REXX, available from the Dynasoft
>Workstation Group. (800)228-0255 or (708)696-4450.  I've never used it, so
>can't answer any questions.

Um..  Not exactly...  Hope you don't mind the update, Barbara.  ;-)
uni-REXX and uni-XEDIT are both products of DYNASOFT.  I once knew the
relationship between DYNASOFT and The Workstation Group, but must 'fess
memory loss (in this respect).  I think DYNASOFT is the parent company,
but don't know for sure (hey, I don't get a cent for this!)  :-(  ;-)

uni-REXX does NOT come with uni-XEDIT, but can of course be ordered too.
Advisable, of course (though there are a couple of freeware/PD/copy-
lefted REXX interpreters for Unix available).  For more on this you'd want
to post to <UREXX-L@Liverpool.ac.uk>; that list includes XEDIT implemen-
tations in its "charter".

uni-XEDIT is quite complete, and implements CMS-XEDIT very nicely on Unix.
Any CMS person who wants to get used to Unix with a few well-known tools at
their fingertips is well-advised to push for uni-XEDIT and uni-REXX.
(And uni-SPF...)

There is a cheaper (not much) XEDIT for unix available from the U. of
Waterloo.  Last I heard (a year ago), it worked only on Suns and AIX.
uni-XEDIT (all of The Workstation Group's prods from CMS) have been
ported to many different (non-)unix platforms.
You might also want to email to Ed Spire <ets@wrkgrp.com>.

Regards.
$$/
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU
X-Acknowledge-To: <JOYCE@IONAACAD>
Newsgroups: bit.listserv.cics-l
Date:         Thu, 17 Dec 1992 21:09:17 EST
From:         Bill Joyce <JOYCE@IONAACAD.BITNET>
Subject:      Integral Systems Payroll/Personnel System

We have migrated to from VSE/SP 4.1 and 3380 dasd to VSE/ESA 1.2.2 and
9345 dasd. All has gone well except for the report generating software,
called A S A P, of this system.

We have received updates from IS but are still unable to get it to work
correctly. We are able to create the data dictionary, but any attempt to
produce even a simple listing results in an E1 error followed by an E5
error.

We are working with IS on this, but they seem as puzzled as we are.
If anyone has any familiarity with this product and can offer some
suugestions, it would be greatly appreciated.

Bill Joyce
Systems Programmer
Iona College
(914) 633-2535
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU
Newsgroups: bit.listserv.cics-l
Date:         Fri, 18 Dec 1992 16:36:45 CST
From:         Larry Holder <##09@UTMARTN.BITNET>
Subject:      more on RETRIEVE question

Simplifying the original question a bit...  I tried where "A" START's
"B" with the FROM option, then does a RETURN to cics.  All "B" has to do
is a RETRIEVE with the INTO option, then RETURN to cics.

When I watch this on CICS with CEDF (I have "B" started associated to a
second terminal, so that I use CEDF on both parts), the RETRIEVE in task
"B" freezes up until task "A" is gone, then completes the RETRIEVE.
I don't understand why...

...Well, they're about to shut the lights for the holidays, so I won't
see my e-mail until December 28th, but if any guru out there can shed
some light on the situation, it would be a great Christmas present.


Larry Holder,  Sr. Programmer/Analyst            Bitnet: ##09@UTMARTN
The University of Tennessee at Martin            Phone:  901-587-7890
Martin, TN  38238                                Fax:    901-587-7841

VM/ESA 1.0, VSE/ESA 1.1, CICS/VSE 2.1, COBOL2, DL/I, SQL/DS, QMF
CICS monitor: Landmark TMON, VSAM compression: Legent EXTEND/DASD
IBM 9221-150, 9336 FBA, 7171, RISC/6000
PSW (Personal Status Words): Saved by grace (Romans 1:16 & 8:38)
From: wsm0@ns1.cc.lehigh.edu (Wayne S. Mery)
Newsgroups: bit.listserv.cics-l
Subject: Controlling TCT entries - terminals/printers
Date: 14 Dec 92 19:44:23 GMT
Organization: Lehigh University

I am looking for a solution for CEST which addresses the two items below or a
no cost alternative to CEST?

We have been using CEST to allow selected personnel to check and change the
status of terminals and printers and purge transactions as needed.

CEST requires the user to specify a supervisory terminal list table (TLT).
The TLT format is restrictive for us.  Among other things:

    1) It is impossible to use against autoinstalled terminals that do not
        follow a naming convention
    2) Does not permit wild cards ==> long lists of terminal ids

Thanks in advance.
Wayne

-- 
-------------------------------------------------------------------------------
Wayne S. Mery           Systems Programmer      Lehigh University Computing Ctr
WSM0@Lehigh.edu  (Unix)                         LUWSM@IBM1.cc.lehigh.edu  (VM)
Comments: Gated by NETNEWS@AUVM.AMERICAN.EDU