HDTenEightyP/NetNews huggingface dataset:
From: mwd@cray.com (Mark Dalton)
Subject: Re: Signal predictions/scanning
Followup-To: mwd@cray.com
Summary: signal scanning
Originator: mwd@snoid
Organization: Cray Research, Inc.
Date: 22 Dec 92 13:48:03 CST

There are a few programs:
        -RegSearch - Searches for regulatory sites.
        -SigSeq - Searches for DNA signal motifs.
        -SignalScan - searches for signal motifs.
        -GM - searches for ORF's, regulation sites, and binding sites.

1. Signal Scan

Analysis of DNA sequences for known eukaryotic signals  LANL.GOV
  SignalScan - searches for signal sequences(Transcription factor DB, TFD)

   Signal scan is a program developed by Dan S. Prestridge, to facilitate the
analysis of DNA sequences for known eukaryotic signals.  This program is free.
You may copy and distribute this program as freely as you wish, but you may
not charge for its distribution.  This program is copyrighted by Los Alamos
National Laboratory and the University of California.
    The source code is written in the `C' language and is fairly easy to port
over to other hardware and operating systems.  The source code will be made
available upon request.
    The author welcomes comments and suggestions, on the program or additions
to the database.  Please contact:

                Dan S. Prestridge
                Los Alamos National Laboratory
                Group T-10, MS K710
                Los Alamos, NM  87545

                E-mail: DXP%LIFE@LANL.GOV

2. SigSeq

 DNA signal sequence searches  - ftp.bio.indiana.edu (129.79.1.101)

3.RegSearch                       Search for DNA regulatory sites
	I think this is also at- ftp.bio.indiana.edu (129.79.1.101)

4. GM (Gene Modeler) searches for ORF's,  regulation sites, and binding sites
	haywire.nmsu.edu

If you need any software feel free to contact me.  Or if you have software
I will try to build a complete list of what is available and what platforms
it runs on.

Thanks!

Mark
-- 
Mark Dalton
Cray Research, Inc.
Eagan, MN 55121
Internet: mwd@cray.com
Newsgroups: bionet.molbio.proteins
From: danj@welchgate.welch.jhu.edu (Dan Jacobson)
Subject: Re: Enzyme Commission Classifications On-Line?
Organization: Johns Hopkins Univ. Welch Medical Library
Date: Wed, 30 Dec 1992 17:49:16 GMT

In article <1992Dec30.161914.26607@welchgate.welch.jhu.edu> danj@welchgate.welch.jhu.edu (Dan Jacobson) writes:
>In article <1992Dec30.091242.18896@husc3.harvard.edu> robison1@husc10.harvard.edu (Keith Robison) writes:
>>Does anyone out there know where I can find the Enzyme Commission 
>>classifications on-line (gopher would be great) or FTPable?
>>
>>
>There is a Wais source with which you can search the EC-enzyme database,
>and of course you can use the wais source through gopher.  (Shameless plug:
>you can find a link to it in the gopher hole at merlot.welch.jhu.edu in the
>
>   -->    4.  Genbank, PIR, Swiss_PROT and other Database Searches/
>
>directory. :-)  Unfortunately the waisserver which runs the searches seems to 
>be down at the moment - I've contacted the maintainer and hope it will be back 
>online soon, if not I may serve it here.
>
>(etc....)

Not often I get to reply to one of my own messages :-).  The waisserver
which serves the EC-Enzyme database is back up.  Thanks and kudos go to 
Thon de Boer for the fast response and quick action.

Happy hunting,

Dan Jacobson

danj@welchgate.welch.jhu.edu

Xref: sparky bionet.molbio.gene-linkage:116 bionet.plants:787
From: cammanly@ubvmsb.cc.buffalo.edu (Ken Manly)
Newsgroups: bionet.molbio.gene-linkage,bionet.plants
Subject: statistics for recombinant inbred strains
Date: 24 Dec 92 14:42:00 GMT
Organization: University at Buffalo
News-Software: VAX/VMS VNEWS 1.41

Recombinant inbred (RI) strains are sets of organisms which have been
derived by inbreeding F2 progeny from a cross of two inbred strains.  For
RI strains of mice, which are created by sib-mating, Haldane and Waddington
showed that

r = R/(4-6R)

where r is the estimated probability of recombination between two Mendelian
loci and R is the proportion of RI strains which are recombinant for those
loci.  For RI strains of plants, which are created by self-pollination,
Haldane and Waddington showed that

r = R/(2-2R)

Green showed that, for RI strains of mice, the variance of r is given by

v = r(1+2r)(1+6r)^2/4N

where v is the estimated variance, N is the number of strains in the set,
and ^ indicates exponentiation.

By analogy with Green's derivation, I find that the variance of r for selfed
RI strains is given by

v = r(1+2r)^2/2N

I'm sure I am not the first to derive this formula.  However, not being a
plant geneticist and not having easy access to most of the plant genetics
literature, I don't know how to find who did derive it.  Can anyone help
me with a reference?

Ken Manly
cammanly@ubvms.cc.buffalo.edu
kmanly@mcbio.med.buffalo.edu
From: ksugiyam@gan.ncc.go.jp (Kenji Sugiyama)
Newsgroups: bionet.molbio.ageing
Subject: (none)
Date: 25 Dec 92 05:25:04 GMT
Distribution: bionet

help
From: kristoff@NET.BIO.NET (David Kristofferson)
Newsgroups: bionet.molbio.ageing
Subject: BIOSCI/bionet Frequently Asked Questions
Date: 1 Jan 93 10:00:02 GMT
Distribution: bionet


New users of BIOSCI/bionet may want to read the "Frequently Asked
Questions" or "FAQ" sheets for BIOSCI.  There are two FAQ sheets for
the newsgroup system.  FAQ I describes the general purpose and uses of
the BIOSCI/bionet newsgroups.  FAQ II provides details on how to
participate in these forums.  Both of these FAQs are available for
anonymous FTP from net.bio.net [134.172.2.69] in
pub/BIOSCI/biosci1.FAQ and pub/BIOSCI/biosci2.FAQ.  They may also be
requested by sending e-mail to biosci@net.bio.net (use plain English
for your request).  The FAQs are also posted on the first of each
month to the newsgroup BIONEWS/bionet.announce immediately following
the posting of the BIOSCI information sheet.

				Sincerely,

				Dave Kristofferson
				BIOSCI/bionet Manager

				kristoff@net.bio.net
From: DSSX@CORNELLA.CIT.CORNELL.EDU
Newsgroups: bionet.molbio.genome-program
Subject: change of address
Date: 30 Dec 92 01:59:00 GMT
Distribution: bionet

To the network coordinator:
  Please change my e-mail address from dssx@cornella.cit.cornell.edu to
craig@macomb.tn.cornell.edu.  The former account has problems receiving
messages.  Thanks, Craig Borkowf.
From: etter%umbsky.dnet@NS.UMB.EDU
Newsgroups: bionet.jobs
Subject: Faculty Position - Population Biologist - UMass
Date: 22 Dec 92 18:36:52 GMT
Distribution: bionet


         FACULTY POSITION AVAILABLE

            POPULATION BIOLOGIST

   University of Massachusetts at Boston

Population Biologist.   The Biology Department of the 
University of Massachusetts at Boston invites 
applications for a tenure-track position 
(assistant professor level) in population 
dynamics or systematics.  Applicants in population 
dynamics should have research expertise in demographic or 
genetic models of populations, metapopulations, host-
pathogen interactions or plant-herbivore systems.  
Applicants in systematics should have research expertise in 
the application of molecular and/or quantitative approaches 
to systematic problems. We are especially interested in 
candidates with interests in environmental issues such as 
conservation and biodiversity.  We seek candidates with 
strong research credentials, including ability to attract 
extramural funding.  In addition to basic research, duties 
will include teaching an advanced course in the area of 
specialization for the new doctoral track in Environmental 
Biology and contributing to established undergraduate 
courses that deal with topics in population biology.  Post-
doctoral experience preferred.  Submit Curriculum Vitae, 
statements of interests and goals in research and teaching, 
and three letters of recommendation to:  Biology Search 
Committee, Department of Biology, University of 
Massachusetts at Boston, 100 Morrissey Boulevard, 
Boston MA 02125-3393. Preference will be given to 
applications received by January 30, 1993.  
An equal opportunity/affirmative action employer.  
Women and minorities are encouraged to apply.
From: dwarhurs@mrc-crc.ac.uk (Dr. D.C. Warhurst)
Newsgroups: bionet.jobs
Subject: Postdoctoral position on Naegleria fowleri
Date: 23 Dec 92 09:13:00 GMT
Distribution: bionet

A post-doctoral scientist is required to work with Dr DC Warhurst on a study of
detection methods for the pathogenic free-living amoeba Naegleria fowleri.
The appointment will be for two years, funded under a contract from the
Department of the Environment.

Candidates should have experience in nucleic acid techniques or antibody work
and aptitude in cell culture, but knowledge of free living amoebae is not ess
essential.
Starting salary will be up to #15,563 plus #2134 London Weighting per annum.

The closing date for applications is 8 Jan 1993. Please send curriculum vitae
with the names of 2 referees to The personnel officer, LSHTM, Keppel St.,
London WC1E 7HT quoting ref DW1.
From: goldie@herald.usask.ca (Hugh Goldie)
Newsgroups: bionet.jobs
Subject: Post Doctoral Position in Genetics
Date: 3 Jan 1993 22:35:49 GMT
Organization: University of Saskatchewan
Distribution: world
NNTP-Posting-Host: herald.usask.ca
Originator: goldie@herald.usask.ca

Applicants should posses a Ph.D. and appropriate background in molecular 
genetics oR cytogenetics.  The area of research involves bovine gene mapping
using chromosome microdissection, lambda librairies, and in situ 
hybridization.  Research collaboration is possible with a small but active
group of researchers, including persons specializing in molecular genetics,
immunogenetics, cytogenetics and embryo transfer/splitting.  The position is
available for one year, with the possibility of renewal.  Applicants are urged
to apply as soon as possibile to come by March 1, 1993.

PLEASE DO NOT REPLY TO THIS ARTICLE OR TO HUGH GOLDIE VIA E-MAIL.

Send c.v. and names of three referees to:

Dr. Shiela Schmutz, Department of Animal Science and Poultry Science, 
University of Saskatchewan, Saskatoon, SK, Canada.  S7K 3J5

Phone:  306-966-4153   Facsimiles:  306-966-4151
Newsgroups: bionet.jobs
From: hammoud@cicb.fr (Mustapha Hammoud)
Subject: Post-doc position wanted
Organization: CICB - Universite' de Rennes I - FR
Date: Sun, 27 Dec 1992 12:14:53 GMT


                                POSITION WANTED
                        ------------------------------
Hi every one,

I am currently rounding up my thesis on a numercial finite elements method to

model arbitrarily shaped Antenna within wide band, the award of a PhD in 

in Telecomunications. My  areas  of  interest  are:  Modelling of Antenna
elements.

Early in the new year (on July 1993), I intend to submit and defend this thesis.

Thereafter, I intend to look for a either a fixed or temporary position
(post-doctorate ...).

I will appreciate any information in this regard or any offer of a job.

Please reply to :

                                 M. HAMMOUD
				 Universite' de Rennes 1
			         Laboratoire Antennes et Re'seaux
				 Avenue du Ge'ne'ral Leclerc
			     	 35042 Rennes - cedex
                                 France


P.S. C.V. and references are available upon request.
 
Regards,..
Newsgroups: bionet.jobs
From: hemeteam@cosy.chem.wsu.edu (James Satterlee)
Subject: Postdoctoral position available
Organization: Washington State University
Date: Thu, 31 Dec 92 22:39:20 GMT

 I have a postdoc position available for an NMR Spectroscopist.  The minimum requirements are a Ph.D. in Chemistry, Biochemistry or Physics with experience in 1D and 2D NMR preferred.  The systems under investigation are paramagnetic metalloproteins involved in oxygen transport, activation and catalysis.  Interested people should contact me at one of the following addresses:
  e-mail to hemeteam@tcosy.chem.wsu.edu
  phone  509-335-8620
  fac    509-335-6687
   Jim Satterlee, Department of Chemistry, Washington State University, Pullman, WA 99164-4630
From: dorand@rbze06.DNET.roche.com ("Daniel M. Doran, PRTC, Phone: 88270")
Newsgroups: bionet.jobs
Subject: F. Hoffmann-La Roche
Date: 21 Dec 92 10:27:16 GMT
Distribution: bionet

PROTEIN CRYSTALLOGRAPHY OPENINGS AT HOFFMANN-LAROCHE, NUTLEY, NJ, USA

We currently have opportunities for a Senior Scientist and an Associate
Scientist to perform research leading to novel pharmaceutical agents based on
the three-dimensional structures of proteins. 

Specific responsibilities include solving structures of relevant proteins such
as receptor-ligand complexes, cell adhesion molecules and a variety of enzymes;
and contributing to the analysis of these structures and their exploitation for
drug design.  In addition, these Scientists will join a dynamic Macromolecular
Structure Group which includes laboratories in protein crystallography;
biomolecular NMR; protein expression, purification and characterization; and
molecular modeling. 

Qualifications for the SENIOR SCIENTIST include a PhD in Biochemistry or a
related field, broad experience in all areas of macromolecular crystallography,
knowledge of protein structure and function, and the ability to perform
collaborative research.  Postdoctoral experience is highly desirable. RESPOND
TO DEPT. EM223VM. 

Qualifications for the Associate Scientist include a BS/MS in Biochemistry/
Chemistry, biochemical skills and experience with proteins. Experience in
crystallizing proteins is desirable, but not required.  RESPOND TO DEPT.
JH233VM. 

For more information see our ad in the December 18th issue of Science or
contact Vincent Madison via e-mail, INET::"madison@rnch01.dnet.roche.com" or
telephone (201) 235-2279. 

To apply, send a letter of application and a resume with salary
history/requirements, indicating the appropriate department, to: STAFFING
DEPARTMENT, HOFFMANN-LAROCHE INC., NUTLEY, NEW JERSEY 07110-1199, USA. 

Newsgroups: bionet.jobs
From: hammoud@cicb.fr (Mustapha Hammoud)
Subject: Post doc position wanted
Organization: CICB - Universite' de Rennes I - FR
Date: Sun, 27 Dec 1992 12:12:24 GMT


                                POSITION WANTED
                        ------------------------------
Hi every one,

  I am currently rounding up my thesis on a numercial finite 
  elements method to model arbitrarily shaped Antenna within 
  wide band, the award of a PhD in Telecomunications. My  
  areas  of  interest  are:  Modelling of Antenna elements.
  Early in the new year (on July 1993), I intend to submit 
  and defend this thesis.
  Thereafter, I intend to look for a either a fixed or temporary 
  position (post-doctorate ...).

  I will appreciate any information in this regard or any offer of a job.

Please reply to :

                                 M. HAMMOUD
				 Universite' de Rennes 1
			         Laboratoire Antennes et Re'seaux
				 Avenue du Ge'ne'ral Leclerc
			     	 35042 Rennes - cedex
                                 France


P.S. C.V. and references are available upon request.
 
Regards,..
From: tac83@isuvax.iastate.edu
Subject: test
Reply-To: tac83@isuvax.iastate.edu
Organization: Iowa State University, Ames, Iowa
Date: Mon, 28 Dec 1992 03:49:10 GMT

test.
test
test.
From: dwarhurs@crc.ac.uk (Dr. D.C. Warhurst)
Newsgroups: bionet.jobs
Subject: RESEARCH FELLOW on detection of Naegleria fowleri
Date: 23 Dec 92 09:53:06 GMT
Distribution: bionet
Original-To: biojobs@uk.ac.daresbury


A post-doctoral scientist is required to work with Dr DC Warhurst
on  a study of detection methods for the pathogenic free-living amoeba
Naegleria fowleri. The appointment will be for two years , funded under a
contract from the Department of the Environment.

Candidates should have experience in nucleic acid techniques or antibody work,
and aptitude in cell culture, but knowledge of free-living amoebae is not ess
essential.

Starting salary will be up to #15,563 plus London Weighting of #2134 per annum.

The closing date for applications is 8 Jan 1993. Please send curriculum vitae
with the names of 2 referees, to the personnel officer, London School of Hygiene aand Tr
Hygiene and tropical Medicine, Keppel St., London WC1E 7HT U.K., quoting ref DW1

Message from Dr. David Warhurst, Dept of Medical Parasitology at the above ad
address. E-mail: dwarhurs@uk.ac.crc
From: aa451@Freenet.carleton.ca (Walford Hewitson)
Newsgroups: bionet.jobs
Subject: greeting
Date: 27 Dec 92 18:48:55 GMT
Organization: National Capital Freenet, Ottawa, Canada


A very good and happy New Year to all at NCF and its users
From: zyu@CGILS.APS.UOGUELPH.CA
Newsgroups: bionet.jobs
Subject: subscription
Date: 22 Dec 92 19:17:48 GMT
Distribution: bionet


	I am trying to subscribe to the EMPLOYMEN newsgroup. Your
consideration will be greatly appreciated. Thanks.
Newsgroups: bionet.jobs
Subject: are double masters a good idea ?
From: babar+@pitt.edu (Jonggu Moon)
Date: 26 Dec 92 22:20:48 GMT
Distribution: bionet
Organization: University of Pittsburgh


Sorry, if this is not the propper group, I don't know a better
place to ask.

I am finishing a Master's in Computer Science
and I am considering starting a Master's in Physical Chemistry.
I am already in a physical chemistry research group
graphically modeling molecules on a workstation.

QUESTION:
  I would like to make a career in computational molecular biology
  especially in applications to the growing gene-technology
  such as the Human Genome Project.

  Is a second master's in chemistry a good idea ? or not ?

Thank you for any opinions and comments.

- jon moon

Xref: sparky bionet.jobs:729 biz.jobs.offered:548 can.jobs:844 misc.jobs.misc:8434
From: states@wucs1.wustl.edu (David States)
Subject: Post-doctoral positions - Institute for Biomedical Computing
Keywords: computational genome statistics post-doctoral
Organization: Washington University, St. Louis MO
Date: Wed, 23 Dec 1992 19:35:30 GMT


Post-doctoral positions are available in the Institute for Biomedical
Computing at Washington University in St. Louis in the general area of
macromolecular modeling and statistical analysis of molecular sequence
data. Research will focus on the development of novel tools and
algorithms for the analysis of molecular sequence data, for the
automation of tertiary structure model building, and for automated
pattern recognition in large databases. Opportunities for collaboration
with large scale sequence projects and human genome mapping and
sequencing centers are available. Knowledge of C programming is
essential and familiarity with statistical analysis of quantitative
data is highly desireable.

The Insitute for Biomedical Computing at Washington University is an
inter-school faculty unit with a 26 year history applying computational
methods to medical and biological research.  Current research
activities include genome sequence studies, quantitative image analysis
and molecular design.  Washington University has a very strong track
record in Human Genome research and the IBC is becoming an integral
part of this effort.  I believe that this will be an area of
challenging and productive research with many opportunities for
individuals with backgrounds ranging from computer science to
biophysics.

To apply, send a letter, e-mail, or FAX with curriculum vitae and 
the names of three references to:

David J. States, Director
Institute for Biomedical Computing
Washington University, Box 8036
700 S. Euclid Ave.
St. Louis, MO   63110

E-mail: states@cs.wustl.edu
FAX: (314) 362-0234

Washington University is an equal opportunity employer.  Women and
minorities are encouraged to apply.
From: torban@csuvax1.csu.murdoch.edu.au (Torban Bennett)
Newsgroups: bionet.jobs
Subject: Lecturer in Enzymology (Australia)
Date: 22 Dec 1992 19:19:22 GMT
NNTP-Posting-Host: csuvax1.csu.murdoch.edu.au
Keywords: Lecturer, Enzymology


Enzymologists with both academic and industrial expertise are invited
to apply for a new position in the Biotechnology Programme.

The appointee will be responsible for developing an undergraduate course
"Bioprocessing and Industrial Enzymology" and will be expected to initiate
research activities in this area.  The appointee will also be required to
contribute to introductory courses in Biochemistry.

Salary Range:$41,000 to $48688

For further details please contact Professor Patrick Carnegie,
email carnegie@murdoch.edu.au

Murdoch University,
School of Biological and Environmental Sciences,
Western Australia.
Newsgroups: bionet.jobs
From: hammoud@cicb.fr (Mustapha Hammoud)
Subject: Post-doc poistion wanted
Organization: CICB - Universite' de Rennes I - FR
Date: Sun, 27 Dec 1992 12:08:06 GMT


                                POSITION WANTED
                        ------------------------------
Hi every one,

I am currently rounding up my thesis on a numercial finite elements method to
model arbitrarily shaped Antenna within wide band, the award of a PhD in 
in Telecomunications. My  areas  of  interest  are:  Modelling of Antenna
elements.
Early in the new year (on July 1993), I intend to submit and defend this thesis.
Thereafter, I intend to look for a either a fixed or temporary position
(post-doctorate ...).

I will appreciate any information in this regard or any offer of a job.

Please reply to :

                                 M. HAMMOUD
				 Universite' de Rennes 1
			         Laboratoire Antennes et Re'seaux
				 Avenue du Ge'ne'ral Leclerc
			     	 35042 Rennes - cedex
                                 France


P.S. C.V. and references are available upon request.
 
Regards,..
From: mffowler@zeus.calpoly.edu (Michael Francis Fowler)
Newsgroups: bionet.plants
Subject: Hydroponics & CO2
Date: 3 Jan 93 23:23:13 GMT
Organization: California Polytechnic State University, San Luis Obispo

I am a Aeroponics/Hydroponics hobbyist.  Currently
I study Horticulture in college.  I am curious about
careers in these related fields.  Any information
about these would be greatly appreciated.  Thanks.
 
Oh...Since I am here-  I am curious what the effects 
of supplementing Carbon Dioxide to my greenhouse
crop of flowers and vegetables.  Any suggestions 
about this is also greatly appreciated.   

	 	 	 	 	 	Have a good one!

	 	 	 		 mffowler@nike.calpoly.edu
From: CFINNEY@UVMVM.BITNET (Chris Finney)
Newsgroups: bionet.plants
Subject: Re: Cocaine: Coca vs. Cocoa?
Date: 26 Dec 92 15:57:22 GMT
Distribution: bionet


>>And now for something completely different;  Cocaine!
>>
>>       I don't work in this area, so I figured a note to the net would be the
>>easiest way to get an easy answer on this question raised by  recent
>>discussions with a friend who is begrudgingly recovering from cocaine
>>adiction.
>>
>>What species is cocaine made from and what is the relationship of this plant
>>to the plant that chocolate is made from?

>Cocaine comes from coca (Erythroxylon coca) and chocolate comes from cacao
>(Theobroma cacao).

Another tidbit for you:

Cacao contains alkaloids of the xanthine family:
      -caffeine       (CNS stimulant)
      -theobromine    (cardiac stimulant)
      -theophylline   (vasodialator)

These are the only known alkaloids in the xanthine family and cocaine is
not one of them.

I would very much recommend the following book for your friend:

''Cacahuatl Eater:  Ruminations of an Unabashed Chocolate Addict''
  By Jonathan Ott

This book is out of print, so please leet me know if your library
hasn't got it and I can tell you where you can get a copy.

                    -Chris Finney, TECH I
                     University of Vermont
Newsgroups: bionet.plants
From: preissj@CLVAX1.CL.MSU.EDU ("J Preiss--Seq Anal")
Newsgroups: bionet.plants
Subject: Cocaine: Coca vs. Cocoa?
Date: 25 Dec 92 19:01:00 GMT
Distribution: bionet

And now for something completely different;  Cocaine!

	I don't work in this area, so I figured a note to the net would be the
easiest way to get an easy answer on this question raised by  recent
discussions with a friend who is begrudgingly recovering from cocaine 
adiction.

What species is cocaine made from and what is the relationship of this plant
to the plant that chocolate is made from?

A related question, but one that does not really pertain to this newsgroup,
does anyone have a breif list of adverse medical side effects of cocaine?
I would prefer physical symptoms, not emotional.

Thanks in advance

		Lenny

		PreissJ@clvax1.cl.msu.edu

Newsgroups: bionet.plants