HDTenEightyP/NetNews huggingface dataset:
From: dab@ray.nlm.nih.gov (Dennis Benson)
Newsgroups: bionet.molbio.genbank,bionet.software
Subject: Re: NCBI Server Format --> FASTA converter
Date: 2 Oct 92 22:06:56 GMT
Organization: National Library of Medicine
X-Newsreader: Tin 1.1 PL4

robison1@husc10.harvard.edu (Keith Robison) writes:
: 
: >Does someone already have a program to convert the results of a
: >NCBI Sequence Server Query into FASTA format?  
: 
: 
: I realize now that I omitted a key qualifier.  GenBank queries
: come back in GenBank format, PIR queries in something that looks
: like PIR format but with some extra linefeeds separating field
: labels from data.  But the Swiss-Prot returns not only have the
: extra line-feeds, but use different heading names than the
: Swiss-Prot distribution (full names rather than abbreviations).
: I guess the real question is whether these deviations will cause
: problems for various programs designed to read/convert PIR and
: Swiss-Prot formats.
: 
: 
: 
: Keith Robison
: Harvard University
: Department of Cellular & Developmental Biology
: Department of Genetics / HHMI
: 
: robison@ribo.harvard.edu 


Keith -- You've pointed out something I want to fix over the next couple
weeks.  The only reason the PIR, Swiss-Prot, (and EMBL) come out looking
a little unfamiliar is that you are seeing the entries as formatted for
IRX text retrieval.

GenBank entries have been passed through a filter to turn them back into
flat-file style records.  I just need to write the filters for the other
databases.  So please, if you can be patient a little longer, don't
write converters for the present output.

I also wonder whether as an interim solution, a FASTA type output option
would take care of some of your needs, ie, do you need all of a PIR
record in PIR format or is your principal need to get an identifier line
and the sequence itself.  It would be easy to have a field in the mail
message 'FASTA yes' or just  'FASTA' and have the program return just
the FASTA-formatted sequence for any of the databases.

Regards,
Dennis Benson
NCBI
From: biogen10@gemini.ldc.lu.se (Bo Servenius)
Newsgroups: bionet.molbio.genbank
Subject: Address to report misstakes in Genbank entry annotation????
Date: 29 Sep 92 18:21:23 GMT
Organization: Lund University, SWEDEN
X-Useragent: Nuntius v1.1

Hello Netters!

I have found a misstake in the annotiaion of a Genbank entry.
Which is the correct address to submit such reports to??

Yours

BOSSE

please respond by email 

biogen10@gemini.ldc.lu.se
From: lmk2@garnet.berkeley.edu
Newsgroups: bionet.molbio.genbank
Subject: Re: Thanks to Yuki Abe
Date: 1 Oct 92 17:40:46 GMT
Distribution: bionet
Organization: University of California, Berkeley
NNTP-Posting-Host: garnet.berkeley.edu


I would like to add my appreciation for Yuki Abe.  I worked
as scientific reviewer for GenBank at the beginning of the
Intelligenetics contract, and she always seemed to me to 
work harder and better than the rest of us, as well as making
my life at IG very pleasant.  Thanks again, Yuki.

Leslie Kay
Graduate Group in Biophysics
Laboratory of Walter J. Freeman
U.C. Berkeley
From: biogen10@gemini.ldc.lu.se (Bo Servenius)
Newsgroups: bionet.molbio.genbank
Subject: Address to report misstakes in Genbank entry annotation????
Date: 29 Sep 92 19:15:16 GMT
Organization: Lund University, SWEDEN
X-Useragent: Nuntius v1.1

Hello Netters!

I have found a misstake in the annotiaion of a Genbank entry.
Which is the correct address to submit such reports to??

Yours

BOSSE

please respond by email 

biogen10@gemini.ldc.lu.se
From: kristoff@GENBANK.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.molbio.genbank
Subject: IntelliGenetics will continue Authorin Support
Date: 29 Sep 92 22:46:00 GMT
Distribution: bionet


Please note that although today is the last day of the full GenBank
contract, IntelliGenetics will continue to distribute and provide
technical support for the Authorin sequence data submission software
for another six months through 31 March 1993.  The Authorin e-mail
address

authorin@genbank.bio.net

will continue to function as will the technical support 800 toll-free
phone number.

				Sincerely,

				Dave Kristofferson
				GenBank Manager

				kristoff@genbank.bio.net
Newsgroups: bionet.molbio.genbank
Subject: Genetic Basis of Nobel Prizes Cloned!!!!
From: robison1@husc10.harvard.edu (Keith Robison)
Date: 1 Oct 92 22:01:10 GMT

	This does not seem to have received much coverage in either the
popular or scientific presses.  Apparently the pathway towards Nobel
Prizedom is finally being elucidated, and it (like many other critical
pathways) involves a protein kinase.  It's amazing what I would miss
if I did not watch bionet.molbio.genbank.updates :-)
	

Keith Robison
Harvard University
Department of Cellular & Developmental Biology
Department of Genetics / HHMI

robison@ribo.harvard.edu 



LOCUS       HUMSKRN      2085 bp ss-mRNA            PRI       29-SEP-1992
DEFINITION  Human nobel serine kinase receptor mRNA, complete cds.
ACCESSION   L02911
KEYWORDS    serine kinase receptor.
SOURCE      Homo sapiens cDNA to mRNA.
  ORGANISM  Homo sapiens
            Eukaryota; Animalia; Chordata; Vertebrata; Mammalia; Theria;
            Eutheria; Primates; Haplorhini; Catarrhini; Hominidae.
REFERENCE   1  (bases 1 to 2085)
  AUTHORS   Matsuzaki,K. and McKeehan,W.L.
  TITLE     nobel serine-kinase receptor type 1
  JOURNAL   Unpublished (1992)
  STANDARD  full staff_entry
From: pgil@TEMIN.LANL.GOV (Paul Gilna)
Newsgroups: bionet.molbio.genbank
Subject: Re: Genetic Basis of Nobel Prizes Cloned!!!!
Date: 2 Oct 92 14:07:13 GMT
Distribution: bionet


sigh!


fixed


--paul
From: pgil@TEMIN.LANL.GOV (Paul Gilna)
Newsgroups: bionet.molbio.genbank
Subject: Re: Genetic Basis of Nobel Prizes Cloned!!!!
Date: 1 Oct 92 23:05:00 GMT
Distribution: bionet


That's how we received it from the authors--we'll check with them to
make sure it's award-winning material.


--paul
From: kristoff@NET.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.molbio.genbank
Subject: Thanks to Yuki Abe
Date: 1 Oct 92 07:01:51 GMT
Distribution: bionet


With all of the "thank you" messages coming in over the last several
days I should call attention to the hardest working person on the
GenBank/IG staff, Yuki Abe, the GenBank Administrator.

Yuki is the only person who worked on the GenBank contract at IG for
the complete five years.  I discovered while writing the final report
that she logged about 20% more total hours on GenBank than anyone
else, including Julie Lawrence who played a major role in the flat
file releases and Authorin development (I was a mere
Johnny-come-lately compared to both of them 8-).

Yuki has handled all of the administrative matters pertaining to tape,
floppy, and CD subscriptions, Authorin distribution, and GOS account
setup, billing, and shutdown.  Her dedication and perseverance was a
key factor in bringing the contract to a smooth close.  Yuki was
assisted at various times during the contract by other fine staffers
including Mary Jo Faulkner, Dan Arbios, Marianne Rocha, Valerie
Yassini, and Peggy Herstine.

Yuki will continue to handle Authorin distribution in the post-GenBank
period, and I am sure that many of you will probably talk to her on the
phone at some time.  I just wanted you all to know what an
extraordinary job she has performed for the biology community.

				Sincerely,

				Dave Kristofferson
				BIOSCI/bionet Manager

				kristoff@net.bio.net
Organization: University of Illinois at Chicago
Date: Sunday, 27 Sep 1992 20:53:25 CDT
From: Li, Dong 312-996-0509 <U53077@uicvm.uic.edu>
Newsgroups: bionet.molbio.genbank
Subject: How to access Brookhave Database?

Dear netters,

I will be grateful if you tell me how to access Brookhave Database (a
protein database) or how to retrieve the files in it.

Thank you for your attention.

Dong LI
*************************************************************************
With malice toward none, with charity for all..........  Abraham Lincoln
=========================================================================
        Dong Li   Telephone: (312) 996-0509    Fax: (312) 413-2435
     Internet: u53077@uicvm.uic.edu     Bitnet: u53077@uicvm.bitnet
Dept. Biological Sciences, Univ. Illinois at Chicago, Chicago, IL 60680
*************************************************************************
Xref: sparky bionet.molbio.genbank:510 bionet.software:1893
From: robison1@husc10.harvard.edu (Keith Robison)
Newsgroups: bionet.molbio.genbank,bionet.software
Subject: Re: NCBI Server Format --> FASTA converter
Date: 4 Oct 92 18:26:21 GMT

dab@ray.nlm.nih.gov (Dennis Benson) writes:

>robison1@husc10.harvard.edu (Keith Robison) writes:
>: 
>: >Does someone already have a program to convert the results of a
>: >NCBI Sequence Server Query into FASTA format?  
>: 

>I also wonder whether as an interim solution, a FASTA type output option
>would take care of some of your needs, ie, do you need all of a PIR
>record in PIR format or is your principal need to get an identifier line
>and the sequence itself.  It would be easy to have a field in the mail
>message 'FASTA yes' or just  'FASTA' and have the program return just
>the FASTA-formatted sequence for any of the databases.

	I won't claim to speak for everyone, but I think this would
be an excellent _permanent_ option.  In my own work, a major reason
for my queries is to get the sequences for use in multiple alignments
and further queries, and so conversion to FASTA format is often my first
operation (since FASTA is probably the most accepted format for analysis
programs).  Actually, being able to specify the return format (FASTA, GCG,
etc) would probably be a feature many people would appreciate.

Keith Robison
Harvard University
Department of Cellular & Developmental Biology
Department of Genetics / HHMI

robison@ribo.harvard.edu 


P.S. -- I (and I suspect many others) would appreciate any suggestions
        for clever UNIX methods to strip out the header on the query returns.
From: kristoff@GENBANK.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.molbio.genbank
Subject: Re: Address to report misstakes in Genbank entry annotation????
Date: 29 Sep 92 23:32:40 GMT
Distribution: bionet

> Hello Netters!
> 
> I have found a misstake in the annotiaion of a Genbank entry.
> Which is the correct address to submit such reports to??
> 
> Yours
> 
> BOSSE
> 
> please respond by email 
> 
> biogen10@gemini.ldc.lu.se
> 
> 

update@genome.lanl.gov
From: karabinos@exmed1.dnet.gwdg.de ("EXMED1::KARABINOS")
Newsgroups: bionet.molbio.proteins
Subject: send-list
Date: 28 Sep 92 09:33:17 GMT
Distribution: bionet
Original-To: proteins@uk.ac.daresbury

send-list
From: karabinos@exmed1.dnet.gwdg.de ("EXMED1::KARABINOS")
Newsgroups: bionet.molbio.proteins
Subject: send-list
Date: 28 Sep 92 09:46:40 GMT
Distribution: bionet
Original-To: proteins@uk.ac.daresbury

send-list
From: Davison@UH.EDU (Dan Davison)
Newsgroups: bionet.molbio.proteins
Subject: Re: How to access Brookhaven database?
Date: 28 Sep 92 13:47:28 GMT
Distribution: bionet

Li, Dong 312-996-0509 said:
> I will be grateful if you tell me how to access Brookhave Database (a
> protein database) or how to retrieve the files in it.

As announced about a month ago, the Protein Data Bank, the
international collection of protein crystallographic coordinates, is
available for anonymous FTP from ftp.bchs.uh.edu in
pub/gene-server/pdb/.... Files are kept compressed, so use binary mode
when FTP'ing.

This service is temporary until the Protein Data Bank gets their own
FTP site arranged.

NOTE: you must know which files you want -- only the coordinate files
are available. No guide to the coordinate files is here.

See the file README for important redistribution information.

dan
gene-server manager
-- 
dr. dan davison/dept. of biochemical and biophysical sciences/univ. of
Houston/4800 Calhoun/Houston,TX 77204-5934/davison@uh.edu/DAVISON@UHOU

-----RIP Isaac Asimov 1920-1992     I'll miss him --------------------

Disclaimer: As always, I speak only for myself, and, usually, only to
myself.
From: GARBERN@SHY.NEURO.UPENN.EDU ("GARBERN")
Newsgroups: bionet.molbio.proteins
Subject: Phosphoaminoacids
Date: 7 Oct 92 02:19:00 GMT
Distribution: bionet

Dear networlders,
At the risk of sounding stupid:
Are there any quick and easy methods for easily distinguishing the different
phosphoamino acids, without having to use HPLC, Mass spec or high voltage
electrophoresis?  For instance, are there any TLC methods?
Thanks, 
Jim Garbern
Neurology
garbern@shy.neuro.upenn.edu
Organization: University of Illinois at Chicago
Date: Sunday, 27 Sep 1992 21:01:35 CDT
From: Li, Dong 312-996-0509 <U53077@uicvm.uic.edu>
Newsgroups: bionet.molbio.proteins
Subject: How to access Brookhave database?

Dear netters,

I will be grateful if you tell me how to access Brookhave Database (a
protein database) or how to retrieve the files in it.

Thank you for your attention.

Dong LI
*************************************************************************
With malice toward none, with charity for all..........  Abraham Lincoln
From: bl275@cleveland.Freenet.Edu (Dan Diaz)
Newsgroups: bionet.molbio.proteins
Subject: Request help on subunit crosslinking
Date: 2 Oct 92 01:24:43 GMT
Reply-To: bl275@cleveland.Freenet.Edu (Dan Diaz)
Organization: Case Western Reserve University, Cleveland, OH (USA)
NNTP-Posting-Host: hela.ins.cwru.edu


I am trying to ascertain the subunit structure of E. coli exonuclease VII,
which is composed of 52 and 9 kDa subunits in an approximate 1:4 ratio.  I
would like to try glutaraldehyde crosslinking and would appreciate any
feedback on methods, protein concentration, NaBH4 quenching,
troubleshooting, etc.
-- 
Dizzy Dan         ddiaz@cwru.bitnet      bl275@cleveland.freenet.edu
Dept. Biochemistry & Wine Tasting  CWRU School of Medicine & Sushi
"I usually like to live in the past, but my time machine is broken"
From: karabinos@exmed1.dnet.gwdg.de ("EXMED1::KARABINOS")
Newsgroups: bionet.molbio.proteins
Subject: list
Date: 26 Sep 92 10:56:25 GMT
Distribution: bionet
Original-To: proteins@uk.ac.daresbury

list bionet.molbio.proteins
From: karabinos@exmed1.dnet.gwdg.de ("EXMED1::KARABINOS")
Newsgroups: bionet.molbio.gene-linkage
Subject: sub
Date: 28 Sep 92 18:11:32 GMT
Distribution: bionet
Original-To: gen-link@uk.ac.daresbury

sub bionet.molbio.gene-linkage
From: bthill@ac.dal.ca
Newsgroups: bionet.molbio.ageing
Subject: Michael Rose
Date: 4 Oct 92 15:21:20 -0300
Organization: Dalhousie University, Halifax, Nova Scotia, Canada

Is Michael Rose out there?  I recently saw him on CNN and he appears to be 
getting younger since he moved to California.

Brian Hill, email bthill@ac.dal.ca
From: chipper@welchgate.welch.jhu.edu (Mike Chipperfield)
Newsgroups: bionet.molbio.genome-program
Subject: Re: microsatellites
Date: 6 Oct 92 14:41:53 GMT
Distribution: bionet
Organization: Johns Hopkins Univ. Welch Medical Library

In article <9210012000.AA04968@net.bio.net> CRHUGHES@VM1.NODAK.EDU (Colin Hughes) writes:
>
>    I am looking for a compilation of data on human microsatellite loci that
>contains the sequence, number and frequency of alleles, size of alleles in bp
>the number of genomes screened and the heterozygosity or PIC values.  Is there
>such a thing?  thanks  Colin.


Colin,

Later on this fall, the latest edition of Genome Maps (edited by Stephen J.
O'Brien, Frederick Cancer Research Institute, Frederick, MD) will be published.
This will have a chapter containing data on all PCR-detected polymorphisms (the
vast majority of which are microsatellites) stored in GDB, as of Sept. 1, 1992.
The data will include primer sequences, max heterozygosity, number of alleles,
cytogenetic location, locus symbol and locus name.

If you need further information regarding this data, please contact me
directly. My email address is: chipper@welchgate.welch.jhu.edu

Sincerely,

Michael A. Chipperfield
DNA Data Coordinator
Genome Data Base
From: whide@kiwi.imgen.bcm.tmc.edu (Winston Hide)
Newsgroups: bionet.molbio.genome-program
Subject: Sequencing/Diagnostics Workshop
Keywords: Sequencing, Diagnostics, Automated Sequencing
Date: 29 Sep 1992 21:18:57 GMT
Reply-To: llawler@bcm.tmc.edu
Organization: Baylor College of Medicine, Institute of Molecular Genetics
Originator: whide@kiwi.imgen.bcm.tmc.edu


 			 ADVANCED AUTOMATED/DIAGNOSTIC DNA SEQUENCING

                  		        WORKSHOP




                                   October 29-31, 1992
                                Baylor College of Medicine
                             Institute for Molecular Genetics
                                  Houston, Texas 77030




Workshop description:

The generation of high quality sequence data has become an essential
tool in molecular biology and diagnostics.  The objective of the
workshop is to provide exposure to the techniques, protocols and
instrumentation currently utilized in the field of automated fluorescent
DNA sequencing.  The workshop will focus upon the areas of high-
throughput, large-scale DNA sequencing and PCR based diagnostic
sequencing.  Automated DNA sequencers (ABI and Pharmacia) as well
as robotic workstations for sequencing and PCR automation (ABI,
Beckman and Perkin Elmer Cetus) will be discussed, demonstrated
and utilized.

The following issues (lab techniques/protocols) will be covered in
discussion, demonstrations and hands-on laboratory work:

I       Template Preparation

        a.      Single strand template preparation by the glass fiber filter
                method.
        b.      Semi-automated PCR template preparation for large-scale
                sequencing.
        c.      PCR template preparation for mutation detection and HIV
                characterization utilizing derivitized/biotinylated PCR
                primers for solid phase sequencing.

II      Sequencing

        a.      Automated cycle-sequencing performed on robotic
                workstations.
        b.      Closure strategies involved in large-scale sequencing
                projects and dye terminator sequencing.
        c.      Solid phase sequencing for mutation detection and
                diagnostics.

III     Examination of Sequence Data

        a.      Error and accuracy
        b.      Diagnostic sequencing for mutation and heterozygote
                detection.
        c.      Troubleshooting DNA sequencing (chemistry and
                instrumentation).

IV      Sequence Assembly

        a.      Overview of available programs for transferring, editing
                and assembling data for large-scale sequencing projects.





Cost of workshop: $750 (Accomodation not included)

Directors:
                Dr. Richard Gibbs and Donna M. Muzny

For further information contact:
Lori Lawler-Lopez, Administrative Coordinator
Telephone:      713-798-5393
FAX:            713-798-5741
email:  llawler@bcm.tmc.edu
From: rdigior@jpmorgan.com (Rinaldo DiGiorgio)
Newsgroups: bionet.molbio.genome-program
Subject: "DNA Search Strings"
Date: 6 Oct 92 17:46:34 GMT
Distribution: bionet

I am looking for some "DNA text strings". I have some parallel search algorithms  
and would like to try them out. Can anyone suggest where I can get some real world  
data from individuals trying to solve real problems.





										Rinaldo
From: CRHUGHES@VM1.NODAK.EDU (Colin Hughes)
Newsgroups: bionet.molbio.genome-program
Subject: microsatellites
Date: 1 Oct 92 19:53:06 GMT
Distribution: bionet
Organization: North Dakota Higher Education Computer Network


    I am looking for a compilation of data on human microsatellite loci that
contains the sequence, number and frequency of alleles, size of alleles in bp
the number of genomes screened and the heterozygosity or PIC values.  Is there
such a thing?  thanks  Colin.
From: rdigior@jpmorgan.com (Rinaldo DiGiorgio)
Newsgroups: bionet.molbio.genome-program
Subject: "DNA Search Strings"
Date: 6 Oct 92 17:49:53 GMT
Distribution: bionet


I am looking for some "DNA text strings". I have some parallel search  
algorithms and would like to try them out. Can anyone suggest where I  
can get some real world data from individuals trying to solve real  
problems.





								 
		Rinaldo
From: buchberg@CALVIN.JCI.TJU.EDU (Dr. Art Buchberg)
Newsgroups: bionet.jobs
Subject: (none)
Date: 5 Oct 92 16:42:01 GMT
Distribution: bionet

NIH funded Postdoctoral positions are available as outlined below. Please 
respond by email to the address listed.


POSTDOCTORAL POSITION 
JEFFERSON CANCER INSTITUTE

A Postdoctoral Position is available immediately to study the role of novel 
oncogenes in contributing to both murine leukemogenesis and development.
 Current research focuses on elucidating the role of two novel genes, Evi-2a and 
Evi-2b, localized within an intron of the neurofibromatosis type 1 (NF1) gene, in 
contributing to  myeloid leukemia as well as todetermine their role in 
development.  Experience in molecular biology and/or biochemical techniques 
desired.  Please send curriculum vitae and the names addresses and telephone 
numbers of three references to:

				Arthur Buchberg, Ph.D.
				Jefferson Cancer Institute
				Thomas Jefferson University
				233 S 10th Street
				Philadelphia, PA 19107
				(215) 955-4533
				(215) 923-4153 (FAX)
				buchberg@calvin.jci.tju.edu (internet)


POSTDOCTORAL POSITION 
JEFFERSON CANCER INSTITUTE


A Postdoctoral Position is available beginning in December of 1992 to study the
 role of novel growth factors that alter susceptibility to various neoplasms and 
affect several developmental processes.  Current research focuses on elucidating 
the role of two genes in contributing to solid tumor formation as well as myeloid 
leukemia.  Experience in molecular biology, genetics and/or biochemical 
techniques desired.  Please send curriculum vitae along with the names, 
addresses and telephone numbers of three references to:


				Linda D. Siracusa, Ph.D.
				Jefferson Cancer Institute
				Thomas Jefferson University
				233 South 10th Street
				Philadelphia, PA 19107
				(215) 955-4536 (phone)
				(215) 923-4153 (fax)
From: skurray@extro.ucc.su.OZ.AU (Ron Skurray)
Subject: Research Assistant (Molecular Genetics)
Organization: /etc/organization
Date: Fri, 2 Oct 1992 01:24:29 GMT



               The University of Sydney

                  Research Assistant

               Molecular Genetics Group

            School of Biological Sciences



The successful applicant will provide assistance for ARC,
NH&MRC and Sydney University Cancer Research Fund supported
projects investigating; bacterial conjugative gene transfer
mechanisms, antibiotic resistance and its evolution in
bacteria and export-protein mediated multidrug resistance.
Techniques in use include all aspects of recombinant DNA
technology, DNA sequencing, PCR, protein analysis.

Applicants should have BSc (Hons) or equivalent with
experience in molecular genetics but applicants with skills
in protein purification/analysis will also be considered.
Position available for one year with possibility of renewal
for up to 2 years subject to funding.


Enquiries to Prof. Skurray (612) 692 2376/FAX (612) 692 4771
or E-mail skurray@extro.ucc.su.oz.au.
Please note that E-mail applications are not acceptable to
the University.

Salary:     Grade I  $24,755-$27,508 p.a.
            Grade II $28,416-$31,027 p.a.

Please note that E-mail applications are not acceptable but
inquires can be made to the above E-mail address

Applications quoting reference no. B39/06 including curriculum
vitae and names, addresses, fax/phone nos. of two referees to
the Assistant Registrar (Appointments), Staff Office (K07),
The University of Sydney, NSW, 2006, (Fax (02) 692 4316) by 15
October 1992.
From: naphade@ATLAS.CHEMISTRY.UAKRON.EDU (Madhavi J Naphade)
Newsgroups: bionet.jobs
Subject: (none)
Date: 5 Oct 92 22:49:54 GMT
Distribution: bionet

I would like to subscribe.
Newsgroups: bionet.jobs