HDTenEightyP/NetNews huggingface dataset:
From: kramer@news.miami.edu (Jack Kramer)
Subject: Re: Apologies for Disappearing Division
Organization: University of Miami, RSMAS
Date: Mon, 21 Dec 92 13:26:27 GMT

In article <BzKxDs.1E1@ncifcrf.gov> toms@fcsparc6.ncifcrf.gov (Tom Schneider) writes:
>In article <1992Dec19.132151.12476@news.miami.edu> kramer@news.miami.edu
>(Jack Kramer) writes:
>
>Because ECORRNB is an unstable name also!!  and so is "16S rRNA"!
>The features are not guaranteed to have a name you put your finger on!!
>
>See my previous message for the requirements placed on the DATABASE ITSELF
>to make any scheme like this become stable and viable!
>
>Thus to use RELATIVE coordinates one must have stable names for objects
>in the database.
>

Wearing a biologist hat, what I would like to really see is:

"Genbank, send me the 16S rRNA gene for E. coli"

Under the NCBI computer hat you say.

"Sorry, until the biologists get their act together and come up
with absolute, stable definitions for everything you can't ask
questions like that.  Some crazy taxonomist might foolishly rename
and reclassify E. coli."

jack
From: kristoff@NET.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.molbio.genbank
Subject: Re: Genbank Complaints
Date: 24 Dec 92 17:55:40 GMT
Distribution: bionet

> With all the (mild) complaints that have been posted, I would just like to
> point out a number of improvements that the NCBI server has over the
> Intelligenetics system:
>  
>     1) The non-redundant database gives you comprehensive search results.
>     2) Service has been significantly faster, even when compared to IG's BLAST
>        server.

I should note that the software is/was essentially the same on both
systems.  The GOS system at IG was running two queues for FASTA, the
BIOSCI news system, and supporting interactive users, in addition to
running two BLAST queues.  Despite all of this load the response was
quite good but definitely not quite as fast as NCBI's current machine
running BLAST.

> Having said that, does anybody know if any other search implementations are
> planned? I grew kind of fond of the BLAZE server at IG during the short period
> it was available (for free).

This service is still available from IG on its BIONET timesharing
service.  We can not offer it for free because we have to pay Maspar
for the use their machine and support our own efforts on this project
without the benefit of a government subsidy since the end of the
GenBank contract.  None of these services have ever been really "free"
when you look at the overall picture.

> And does anybody have any comments regarding the
> _practical_ advantages of the various search strategies- ie FASTA, BLAST,
> BLAZE.
>  

Doug Brutlag has studied this issue and perhaps would like to share
some of his results.

> Happy Holidays,  Michael McKenna MCKMICP@YaleVM.YCC.Yale.edu

Same to you!

				Sincerely,

				Dave Kristofferson
				former GOS manager

				kristoff@net.bio.net
From: doelz@comp.bioz.unibas.ch (Reinhard Doelz)
Newsgroups: bionet.molbio.genbank,bionet.molbio.embldatabank
Subject: Re: EMBL <> GenBank
Date: 23 Dec 92 08:16:43 GMT
Reply-To: doelz@urz.unibas.ch
Organization: EMBnet Switzerland [BASEL]

In article <1992Dec22.220954.563@nlm.nih.gov>, ostell@object.nlm.nih.gov (Jim Ostell) writes:
|> Actually there are a large number of differences between EMBL and
|> GenBank, including entries with the same primary accession but
|> different sequences in EMBL and GenBank, entries with the same
|> sequence but different primary accessions in EMBL and GenBank,
|> and all sorts of other varients.  There are a variety of reasons
...

It has been brought to our attention by one of our customers that there 
are currently thousands (!) of these cases. In contrast to the original 
assumption that Genbank 74 will now be sort of identical to EMBL 33, I 
can only warn all of you who trusted in this rather than trying it out. 

Actually, if you take one of the applications doing accession number 
exclusion (I use the GCG package for this purpose here), I get more 
than 10000 entries which show accession numbers that are not in EMBL 33
but in GENBANK 74 ... the listing keyed by division is shown here: 

Gb_Ba:
     Entries:   1,715   Accession Numbers:  2,692
Gb_In:
     Entries:   1,037   Accession Numbers:  1,494
Gb_Om:
     Entries:     446   Accession Numbers:    634
Gb_EST:
     Entries:   1,000   Accession Numbers:  1,000
Gb_Ov:
     Entries:     487   Accession Numbers:    694
Gb_Ph:
     Entries:      76   Accession Numbers:    134
Gb_Pl:
     Entries:   1,707   Accession Numbers:  2,512
Gb_Pr:
     Entries:   3,096   Accession Numbers:  3,743
Gb_Ro:
     Entries:   1,933   Accession Numbers:  2,601
Gb_St:
     Entries:      61   Accession Numbers:     63
Gb_Sy:
     Entries:       5   Accession Numbers:      5
Gb_Un:
     Entries:       8   Accession Numbers:      8
Gb_Vi:
     Entries:     747   Accession Numbers:    938

The statistics read as follows: 

Numbers       	total   Primary numbers
D...		 1093 	1027
J... 		 15 	3
K... 		 4 	2
L... 		 219 	219
M... 		 966 	107
S... 		 2900   2899
V... 		 3      0
X... 		 468    6
Z... 		 30     6

Total            5698   4269

The only thing which is not clear to me is, then, why these 5700 numbers
are present in more than 15000 Genbank entries. Clearly a point where 
a cleanup might be necessary... 

Regards
Reinhard

-- 
+----------------------------------+-------------------------------------+
|    Dr. Reinhard Doelz            | RFC     doelz@urz.unibas.ch         |
|      Biocomputing                | DECNET  20579::48130::doelz         |
|Biozentrum der Universitaet       | X25     022846211142036::doelz      |
|   Klingelbergstrasse 70          | FAX     x41 61 261- 6760 or 267- 2078     
|     CH 4056 Basel                | TEL     x41 61 267- 2076 or 2247    |   
+------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+
               -----------------------------------------
From: shibumi@net.bio.net (Kenton A. Hoover)
Newsgroups: bionet.molbio.genbank
Subject: Re: bionet.molbio.genbank.updates resumes
Date: 29 Dec 92 01:40:18 GMT
Reply-To: shibumi@net.bio.net
Distribution: bionet
Organization: BIOSCI International Newsgroups for Biology

There was a short break over Christmas weekend, since the 'back' updates have
to be inserted by hand. 

One day last week a large number of duplicate entries were injected into the
news stream.  This was due to a software bug (actually, a permissions problem),
and has been fixed.  No ill effects should have resulted from the duplicates.

We hope to be current on updates by the 5th of January. 

| Kenton A. Hoover                                 |      shibumi@net.bio.net |
| BIOSCI Network Administrator                     |                          |
| BIOSCI/IntelliGenetics, Inc.                     |          +1 415 962 7300 |
|=========== net.bio.net -- The New Home of the bionet Newsgroups ============|
Newsgroups: bionet.molbio.genbank
From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert)
Subject: Re: Apologies for Disappearing Division
Organization: Biology, Indiana University - Bloomington
Date: Mon, 21 Dec 1992 23:14:16 GMT

In article <1992Dec21.132627.17314@news.miami.edu> kramer@news.miami.edu (Jack Kramer) writes:
>Wearing a biologist hat, what I would like to really see is:
>
>"Genbank, send me the 16S rRNA gene for E. coli"

We are getting close to that now.  I just tried your question on
the Gopherized copy of Genbank here at IUBio, with these results:

  Search GenBank: Genbank, send me the 16S rRNA gene for E. coli

1.  K01983 Anacystis nidulans partial 16S rRNA, Ile-tRNA and Ala-tRNA genes;.
2.  X12420 Escherichia coli DNA for 16S-23S intergenic region..
3.  M29364 E.coli ATP-dependent protease binding subunit (clpB) gene, compl.
4.  J01694 E.coli rRNA operon (rrnA) coding for 16S rRNA, promoter region..
5.  J01695 E.coli rRNA operon (rrnB) coding for Glu-tRNA-2, 5S, 16S and 23S.
6.  M10739 E.coli rrnC operon promoter region and 16S rRNA gene 5'end..
7.  J01692 E.coli rRNA operon (rrnD*) gene coding for 16S rRNA, promoter.
8.  J01702 E.coli rRNA operon (rrnD*) coding for ile-tRNA-1, ala-tRNA-1B and.
9.  J01697 E.coli rRNA operon (rrnE) coding for 16S rRNA, promoter..
10. J01700 E.coli rRNA operon (rrnx: rrnG or rrnF), coding for 16S rRNA,.
11. K00763 E.coli rRNA operon (rrnX), coding for ile-tRNA-1,ala-tRNA-1B and.
12. V00330 E. coli gene rrnA for 16S ribosomal RNA.
13. K01056 E.coli 16s rrna gene (partial)..
14. K01057 E.coli 16s rrna (3' end) & ile-trna-1 genes..
15. M58020 Mycobacterium leprae 16S rRNA gene, 5' end..
16. S39788 16S rRNA [Escherichia coli, subsurface soil, cluster III, rRNA.
17. M87484 Tropheryma whippelii homologue to Escherichia coli 16S rRNA (from.
18. X01339 Bombyx mori 18S rRNA gene, 3' end..
19. V01390 Trypanosoma brucei kinetoplast DNA maxicircle fragment encoding .
20. X12890 E.gracilis rrnC operon 16S, 23S and 5S rRNA, tRNA-Ile and tRNA-A.
21. V00653 A. nidulans mitochondrial genes for 16S rRNA and tRNA-Tyr (conta.
22. J01390 a.nidulans mt dna between h2/h5 & bh2/b2 junctions. genes for.
23. Z00028 Zea mays chloroplast rRNA-operon.
24. M59073 Campylobacter coli 16S ribosomal RNA..
25. L04312 Campylobacter coli, complete 16S ribosomal RNA..
26. M25458 E.coli 23S rRNA..
27. J01859 E.coli 16S ribosomal RNA..
28. M35308 E.coli 16S rRNA fragment..
29. M35309 E.coli 16S rRNA fragment..
30. M25588 E.coli 16S rRNA..
31. M25051 E.coli T1 ribonuclease sensitive 16S rRNA region, segment 1..
32. M25052 E.coli T1 ribonuclease sensitive 16S rRNA region, segment 2..
...

This searching software (WAIS) is designed to handle english language queries
such as yours, and it generally works pretty well.  You still have to weed out
the ones you don't want from this selection.
-- 
Don Gilbert                                     gilbert@bio.indiana.edu
biocomputing office, biology dept., indiana univ., bloomington, in 47405
From: ostell@object.nlm.nih.gov (Jim Ostell)
Newsgroups: bionet.molbio.genbank
Subject: Re: EMBL <> GenBank
Date: 22 Dec 92 22:09:54 GMT
Organization: National Library of Medicine
X-Newsreader: Tin 1.1 PL4

Actually there are a large number of differences between EMBL and
GenBank, including entries with the same primary accession but
different sequences in EMBL and GenBank, entries with the same
sequence but different primary accessions in EMBL and GenBank,
and all sorts of other varients.  There are a variety of reasons
for these problems.  One of the first uses of the ID database
will be to begin to sort these out.

One of the first effects of this you will see, is for entries
with EMBL primary accessions to come directly from EMBL, DDBJ
from DDBJ.  This will solve the specific problems you allude
to, but not some of the deeper ones.

  Jim Ostell
  NCBI
Xref: sparky bionet.molbio.genbank:593 bionet.molbio.embldatabank:63
From: MCKMICP@YaleVM.YCC.Yale.Edu (Michael McKenna)
Newsgroups: bionet.molbio.genbank
Subject: Genbank Complaints
Date: 23 Dec 92 03:17:04 GMT
Organization: Yale University

With all the (mild) complaints that have been posted, I would just like to
point out a number of improvements that the NCBI server has over the
Intelligenetics system:
 
    1) The non-redundant database gives you comprehensive search results.
    2) Service has been significantly faster, even when compared to IG's BLAST
       server.
    3) The retrieve server has boolean controls as well as field restrictions
       which allow you to refine an accurate search strategy. For these
       reasons, it doesn't really matter how the database is organized, as
       long as there are enough accurate descriptions in each file.
    4) The NIH gopher server, which may or may not be connected to the NCBI,
       allows you to peruse up-to-date databases in a very convenient format,
       although its search algorithms are not as powerful as Retrieve.
 
 
Personally, I am quite pleased with the changes, and look forward to continued
improvements as the databases grow, and as computers, software, and biosearch
algorithms improve.
 
Having said that, does anybody know if any other search implementations are
planned? I grew kind of fond of the BLAZE server at IG during the short period
it was available (for free). And does anybody have any comments regarding the
_practical_ advantages of the various search strategies- ie FASTA, BLAST,
BLAZE.
 
Happy Holidays,  Michael McKenna MCKMICP@YaleVM.YCC.Yale.edu
From: S911896@VAX.CSC.CUHK.HK
Newsgroups: bionet.molbio.genbank
Subject: (none)
Date: 4 Jan 93 03:23:00 GMT
Distribution: bionet

Dear Sirs,

I want to contact Keiko Ozato of lab of developmental and molecular immunity, national institute of child health and human development, National Institute of Health, Bethesda, MD 20892. I shall have a discussion about his/her published
paper. Please give me his/her e mail address.

Thank you in advance.

Sincerely,

Qiu Yaowu
Dept of Biology, The Chinese University of Hong Kong, Hong Kong.
From: harper@convex.csc.FI (Rob Harper)
Subject: Re: Apologies for Disappearing Division
Organization: Finnish Academic and Research Network Project - FUNET
Date: Tue, 22 Dec 92 11:06:27 GMT

In <Bzn2A6.559@ncifcrf.gov> toms@fcs260c2.ncifcrf.gov (Tom Schneider) writes:

>Ever hear of Sisyphus?  It's exactly the same.  We analyzed nearly 1800 human
>splice junctions. The database changed. We are now again at the bottom of the
>splice junction hill.  

I did a WAIS search on Sisyphus on GenBank and EMBL databank's and
apparently they have never heard of him ;-)

Sisyphus: A character from classical Greek mythology, the king of Corinth
          who was renowned for his cunning. He was so quick-witted that he
          even cheated the god of death Hades.
          As a punishment for this "crime" Sisyphus had to roll a huge
          heavy stone to the top of a mountain, but each time he nearly
          reached the top, the stone would slip away from him and roll
          down to the bottom once again. From this myth comes the phrase
          "The work of Sisyphus" meaning work that is unending and never
          gives any results.

Rob "Mutato nomine, de te fabula narratur." Harper

--
 ~ Rob Harper                    ~ E-mail:          harper@convex.csc.fi    
 ~ Finnish State Computer Centre ~ Molbio/software: harper@nic.funet.fi
 ~ P.O. Box 40                   ~ Telephone:       +358 0 457 2076
 ~ SF-02101 Espoo Finland        ~ Fax:             +358 0 457 2302
Newsgroups: bionet.molbio.genbank
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Subject: Re: Apologies for Disappearing Division
Organization: Frederick Cancer Research and Development Center
Date: Mon, 21 Dec 1992 22:29:08 GMT

In article <1992Dec21.132627.17314@news.miami.edu>
kramer@news.miami.edu (Jack Kramer) writes:

| Wearing a biologist hat, what I would like to really see is:
| "Genbank, send me the 16S rRNA gene for E. coli"

Right - except that one would also have to specify which one (there
are 7 operons).  Presumably one would either get an objection or one
would get a book containing all of them.  (Also, you need to specify
the strain.)

| Under the NCBI computer hat you say.
| "Sorry, until the biologists get their act together and come up
| with absolute, stable definitions for everything you can't ask
| questions like that. Some crazy taxonomist might foolishly rename
| and reclassify E. coli."

This objection gets raised every time.  The solution is simple: allow synonyms,
and flag the old usage for the person.  This is no problem to the people
working on the genetics of an organism - there comes to be a standard agreed
set of names.  We can use---and extend---those standard names for sequence
databases like GenBank.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
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 16:19:14 GMT

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.

If you'd like to ftp the whole database you can get it from (among other places)
ncbi.nlm.nih.gov in the repository/enzyme directory, or (shameless plug :-)
go to the gopher hole at (among other places) merlot.welch.jhu.edu and
go into the 

   -->    2.  FTP Sites For Biology/

directory where there is a link into the ncbi site - 

( 16. NCBI Repository FTP Archive /)

in which you'll find the enzyme directory and the EC-enzyme database
which you can retrieve - it will take a little while as the database
is an 800K file - some gopher clients handle big files better than others.


Best of luck and Happy New Year,

Dan Jacobson

danj@welchgate.welch.jhu.edu
Xref: sparky bionet.molbio.proteins:284 bionet.software:2328
Organization: University of Illinois at Chicago
Date: Friday, 25 Dec 1992 09:41:43 CST
From: Dong Li 312-996-0509 <U59918@uicvm.uic.edu>
Newsgroups: bionet.molbio.proteins,bionet.software
Subject: How to display 3D structure of PDB files with a PC?

Dear Netters,

I am trying to do the tertiary modeling now. I will be very grateful
if you tell me how I can get a program to display with an IBM PC
the tertiary or stereo structures of the proteins, based on the
data files from Brookhaven Protein Database.

Any help will be appreciated very much.

By the way, thanks a lot to those who helped me previously.
Due to the uncertain network problem, I failed to reply and say THANK YOU
to some of them.

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
*************************************************************************
Newsgroups: bionet.molbio.proteins,bionet.software
From: S911896@VAX.CSC.CUHK.HK
Newsgroups: bionet.molbio.proteins
Subject: (none)
Date: 4 Jan 93 02:42:00 GMT
Distribution: bionet

Dear nectters,

If you know what are the transcriptional factors of GCN4, steroid binding 
protein gene, or other growth regulatory factor genes, please let me known
as soon as possible. I am doing related analyses.

Thank you for your great helps.

Sincerely,

Qiu Yaowu
Chinese university of Hong Kong
From: rdoelz@comp.bioz.unibas.ch (Reinhard Doelz [remote])
Newsgroups: bionet.molbio.proteins
Subject: Re: Enzyme Commission Classifications On-Line?
Date: 31 Dec 92 12:05:44 GMT
Organization: EMBnet Switzerland [Basel]

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?

on the bioftp GOPHER server the ENZYME database is indexed and available
for searching via gopher (port 70 on bioftp.unibas.ch). 

bioftp.unibas.ch gets also updated by Dr. Bairoch, to whom I am very grateful, 
in the framework of the European Molecular Biology Network, Swiss node, 
in the directory archive_data/database by anonymous ftp. The same
server [131.152.8.1	for those without name server] has the 
EMBL CD-ROM mounted and therefore the current EMBL Version of the 
ENZYME database on-line. 

The host biomed.uio.no provides telnet login under the username srs 
(as managed by R.Lopez, srs is copyright T.Etzold) where you can 
search several molbio databases including xref annotation. 

Regards 
Reinhard 


-- 
+----------------------------------+-------------------------------------+
|    Dr. Reinhard Doelz            | RFC     doelz@urz.unibas.ch         |
|      Biocomputing                | DECNET  20579::48130::doelz         |
|Biozentrum der Universitaet       | X25     022846211142036::doelz      |
From: s911896@HP720A.CSC.CUHK.HK
Newsgroups: bionet.molbio.proteins
Subject: (none)
Date: 2 Jan 93 09:55:14 GMT
Distribution: bionet

Dear nectters,

I have a question, below.

What are the transcriptional factors of hormone receptor genes, such
as the estrogen receptor gene(in human or other animals). Moreover,
please give me a clue about how to find related paper.

I am looking forward to hearing your as-soon-as-possible reply.
thank you in advance.

Sincerely,
Qiu Yaowu
Chinese University of Hong Kong
From: cherry@OPAL.MGH.HARVARD.EDU
Newsgroups: bionet.molbio.proteins
Subject: Re: Enzyme Commission Classifications On-Line?
Date: 30 Dec 92 23:31:16 GMT
Reply-To: cherry@OPAL.MGH.HARVARD.EDU
Organization: Molecular Biology - Mass Gen Hospital

Here is a description of Amos Bairoch's ENZYME database from the
ENZYME User's Manual.


   Amos Bairoch
   Medical Biochemistry Department
   Centre Medical Universitaire
   1211 Geneva 4
   Switzerland

   Telephone: (+41 22) 361 84 92
   Electronic mail address: BAIROCH@CMU.UNIGE.CH
                         or BAIROCH@CGECMU51.BITNET


   1.1) Definition of the scope of the data bank

   The 'ENZYME'  data bank  contains the  following data  for each  type of
   characterized enzyme for which an EC number has been provided:

   -  EC number.
   -  Recommended name.
   -  Alternative names (if any).
   -  Catalytic activity.
   -  Cofactors (if any).
   -  Pointers to  the SWISS-PROT  entrie(s) that  correspond to the enzyme
      (if any).
   -  Pointers to disease(s) associated with a deficiency of the enzyme (if
      any).

   We believe  that the  ENZYME data bank will be useful to anybody working
   with enzymes  and will allow programs to be developed that can help with
   the creation of new metabolic pathways.


   1.2) Sources of the data

   The main  source for  the data  in  the  ENZYME  data  bank  comes  from
   recommendations of the Nomenclature Committee of the International Union
   of Biochemistry  (NC-IUB) [1,2,3,4].  A minor part of the data  has been
   extracted from the literature.

   [1]  Enzyme Nomenclature, NC-IUB, Academic Press, New-York, (1984).
   [2]  Supplement 1: corrections and additions.
        Eur. J. Biochem. 157:1-26(1986).
   [3]  Supplement 2: corrections and additions.
        Eur. J. Biochem. 179:489-533(1989).
   [4]  Supplement 3: corrections and additions.
      Eur. J. Biochem. 187:263-281(1990).
Newsgroups: bionet.molbio.proteins
Subject: Enzyme Commission Classifications On-Line?
From: robison1@husc10.harvard.edu (Keith Robison)
Date: 30 Dec 92 09:12:42 EST
Organization: Harvard University Science Center

Does anyone out there know where I can find the Enzyme Commission 
classifications on-line (gopher would be great) or FTPable?


Thanks.


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

robison@biosun.harvard.edu 




Newsgroups: bionet.molbio.proteins