HDTenEightyP/NetNews huggingface dataset:
From: dab@ray.nlm.nih.gov (Dennis Benson)
Newsgroups: bionet.molbio.genbank
Subject: Re: Apologies for Disappearing Division
Date: 16 Dec 92 21:07:59 GMT
Organization: National Library of Medicine
X-Newsreader: Tin 1.1 PL4

brianf@dna.uvm.edu (Brain Foley) writes:
: So the organelle division is gone, and all those entries are now
: merged in with the organism in which the organelle lives.
: 
: I am interested in comparing the mutation rates and
: transversion:transition ratios of eukaryotic DNA, oganellar DNA and
: bacterial DNA.  Can someone supply me with some C++ source code to
: separate the eukaryotic entries from the organellar entries?
: --


Brian -- We don't have source code to do the separation, but we
do have a file which identifies all previous entries in the Organelle
division and the division to which they have migrated.  The file is
named 'migrat74.div' and is located in the directory ./ncbi-genbank
on the anonymous FTP server:  ncbi.nlm.nih.gov

The file also contains entries that migrated from the previous NLM
division as well as those which migrated into the new EST division.

Hope this may be of some help.

Dennis Benson
NCBI
From: ernest@lenti.med.umn.edu (Ernest Retzel (1535 49118))
Newsgroups: bionet.molbio.genbank
Subject: Re: Apologies for Disappearing Division
Date: 18 Dec 92 14:43:42 GMT
Organization: University of Minnesota

> I think that
> as we obtain more sequence data, then the curators of that data ought
> to help those who analyze the data by providing the data in logical
> catagories without having to re-invent something that at one time
> existed.  As the sequencing and mapping proceed, we might even have
> gb_huchrom1, gb_huchrom2, etc, ...... as separate catagories.  I know
> this makes for lots of catagories, but sure is helpful for those 
> interested in a more focused sub-set of the data.

I would take issue with this; the variations of flat file "databases of
interest" is pretty much infinite.  A reliable means of creating those
databases on the fly is really more the appropriate.  Or simply a "view" 
into the database, without the creation of a real or even virtual separate 
entity.

[I didn't appreciate the change either, but more because I didn't appreciate
the surprise; we haven't had one of those for many years.]

Ernie Retzel

ernest@lenti.med.umn.edu
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: Thu, 17 Dec 1992 19:25:05 GMT

In article <1992Dec16.210759.23234@nlm.nih.gov> dab@ray.nlm.nih.gov
(Dennis Benson) writes:

>brianf@dna.uvm.edu (Brain Foley) writes:
>: So the organelle division is gone, and all those entries are now
>: merged in with the organism in which the organelle lives.

I should laugh but it is too sad.  Perhaps some of you recall that the design
of Delila was into these things called "organisms" and then those had parts
called "chromosomes".  In Delila the solution is trivial:

organism H.sapiens;
chromosome 3;
gene ...

The first two instructions specify all know sequences on chromosome 3 of the
"cononical" human sequence (one would specify "strain" if one wanted a sequence
that wasn't from the black female who represents the cononical ... ;-)

The trouble is that the structure of GenBank is a huge pile of these things
called "entries" which really don't have much connection to each other.  Having
just knocked out some of the divisions was trivial because THERE IS NO
DEFINITION OF GENBANK so the horrible philosophical violation was not debated,
nor even debatable!

The solution is to have a data item in each "entry" that indicates the
chromosome and the map location of the sequence.  Then we can avoid extracting
those from organelles with a simple IF statement.

As I said in the other news group, there is a new version of my paper on the
Philosophy of GenBank in ncifcrf.gov/pub/delila/philgen*.  Comments welcome.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: bickle@urz.unibas.ch
Newsgroups: bionet.molbio.genbank
Subject: Re: Apologies for Disappearing Division
Date: 18 Dec 92 11:35:13 MET
Organization: University of Basel, Switzerland

In article <17DEC199206391726@aardvark.ucs.uoknor.edu>, broe@aardvark.ucs.uoknor.edu (Bruce Roe) writes:
>>brianf@dna.uvm.edu (Brain Foley) writes:
>>: So the organelle division is gone, and all those entries are now
>>: merged in with the organism in which the organelle lives.
>>: 
>      [stuff deleted]
> 
> Hi all,
> 	I really don't want to start an argument here, but I for one
> think that removing the organelle division and merging the data into
> the division where the organelle "lives" is a step backwards.  Maybe
> there are logical reasons for this but they escape me.  I think that
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

I agree, taxonomically it makes no sense. The organelles are more
closely related to each other than they are to the nuclear genomes
of the cells in which they reside. 


#include sig.lis
Newsgroups: bionet.molbio.genbank
From: brianf@dna.uvm.edu (Brain Foley)
Subject: Re: Re: Apologies for Disappearing Division
Organization: Division of EMBA, University of Vermont
Date: Wed, 16 Dec 1992 16:14:46 GMT

So the organelle division is gone, and all those entries are now
merged in with the organism in which the organelle lives.

I am interested in comparing the mutation rates and
transversion:transition ratios of eukaryotic DNA, oganellar DNA and
bacterial DNA.  Can someone supply me with some C++ source code to
separate the eukaryotic entries from the organellar entries?
--
********************************************************************
*  Brian Foley               *     If we knew what we were doing   *
*  Molecular Genetics Dept.  *     it wouldn't be called research  *
*  University of Vermont     *                                     *
********************************************************************
Newsgroups: bionet.molbio.genbank
From: kramer@news.miami.edu (Jack Kramer)
Subject: Re: Apologies for Disappearing Division
Organization: University of Miami, RSMAS
Date: Sat, 19 Dec 92 13:21:51 GMT

In article <18DEC199212080223@seqvax.caltech.edu> mathog@seqvax.caltech.edu (David Mathog) writes:
>In article <BzGILx.41C@usenet.ucs.indiana.edu>, gilbertd@sunflower.bio.indiana.edu (Don Gilbert) writes...
>
>As a start, I'd really like to see NCBI RETRIEVE implement the following
>(never mind the syntax). 
>
>  SEND <entry number> [ FROM <START> TO <END> ]
>
>For the sequence this is a trivial operation.  Chopping out the appropriate
>parts of the reference section *should* be possible too, if maybe a bit 
>more challenging.
>

The <START> and <END> could vary as sequences are combined into complete
chromosome entries.  Why not tie such requests together using the
FEATURE entries?

SEND <entry number||name> <FEATURE>

For example:

SEND ECORRNB "16S rRNA"

jack
Newsgroups: bionet.molbio.genbank
From: toms@fcsparc6.ncifcrf.gov (Tom Schneider)
Subject: Re: Apologies for Disappearing Division
Organization: Frederick Cancer Research and Development Center
Date: Sun, 20 Dec 1992 22:34:40 GMT

In article <1992Dec19.132151.12476@news.miami.edu> kramer@news.miami.edu
(Jack Kramer) writes:

|In article <18DEC199212080223@seqvax.caltech.edu> mathog@seqvax.caltech.edu (David Mathog) writes:
|>In article <BzGILx.41C@usenet.ucs.indiana.edu>, gilbertd@sunflower.bio.indiana.edu (Don Gilbert) writes...
|>
|>As a start, I'd really like to see NCBI RETRIEVE implement the following
|>(never mind the syntax). 
|>
|>  SEND <entry number> [ FROM <START> TO <END> ]
|>
|>For the sequence this is a trivial operation.  Chopping out the appropriate
|>parts of the reference section *should* be possible too, if maybe a bit 
|>more challenging.
|>
|

|The <START> and <END> could vary as sequences are combined into complete
|chromosome entries.  Why not tie such requests together using the
|FEATURE entries?
|
|SEND <entry number||name> <FEATURE>
|
|For example:
|
|SEND ECORRNB "16S rRNA"
|
|jack

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.

Finally, one WILL sometimes want to be able to specify a location in ABSOLUTE
coordinates, knowing full well that such instructions are not the best and are
not as stable as RELATIVE coordinates.  But for a quick-and-dirty piece of
work, they would be useful.  Also, search results usually will be reported in
absolute coordinates (although the idea of reporting the locations of EcoRI
sites relative to gene starts in E. coli is a new one for me!  Wow!)

  Tom "Cassandra-Delila" Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: dab@ray.nlm.nih.gov (Dennis Benson)
Newsgroups: bionet.molbio.genbank
Subject: Re: Release 74 of GenBank Available
Date: 11 Dec 92 19:12:15 GMT
Organization: National Library of Medicine
X-Newsreader: Tin 1.1 PL4

stoehr@embl-heidelberg.de writes:
: In article <1992Dec10.190122.22069@nlm.nih.gov>, dab@ray.nlm.nih.gov
: (Dennis Benson) writes:
: > Because NCBI handles discrete update streams from LANL, DDBJ, and
: > EMBL, it is difficult to guarantee the uniqueness of LOCUS names
: > among all sequence entries. With release 74.0, we were unable to
: > resolve 5 duplicate names before close-of-data:
: >...
: 
: Just to be clear - the difficulty is with you and your RDBMS, rather than
: the discrete data streams ?

Peter -- Agreed, the statement above is not very clear; the problem
essentially was that two different streams used the same locus name.
What we need to do, and of course will do, is resolve these conflicts
by getting back to the databases concerned well before we're caught
up in trying to meet deadlines for the production release. 

: 
: > We have decided to allow the LOCUS name redundancy rather than filter
: > out the sequences involved.
: 
: For just this release 74 or in the future also ?
: 
: Peter Stoehr
: EMBL Data Library

As indicated above, hopefully release 74 will be the last time this occurs.

Dennis Benson
NCBI
From: ernest@lenti.med.umn.edu (Ernest Retzel (1535 49118))
Newsgroups: bionet.molbio.genbank
Subject: Re: Apologies for Disappearing Division
Date: 18 Dec 92 16:11:50 GMT
Organization: University of Minnesota

> I think that
> as we obtain more sequence data, then the curators of that data ought
> to help those who analyze the data by providing the data in logical
> catagories without having to re-invent something that at one time
> existed.  As the sequencing and mapping proceed, we might even have
> gb_huchrom1, gb_huchrom2, etc, ...... as separate catagories.  I know
> this makes for lots of catagories, but sure is helpful for those 
> interested in a more focused sub-set of the data.

I would take issue with this; the variations of flat file "databases of
interest" is pretty much infinite.  A reliable means of creating those
databases on the fly is really more the appropriate.  Or simply a "view" 
into the database, without the creation of a real or even virtual separate 
entity.

[I didn't appreciate the change either, but more because I didn't appreciate
the surprise; we haven't had one of those for many years.]

Ernie Retzel

ernest@lenti.med.umn.edu

[If you see this twice, sorry]
From: kristoff@NET.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.molbio.genbank
Subject: Re: Submitting DNA sequence data from a SUN
Date: 18 Dec 92 21:52:43 GMT
Distribution: bionet

> 
> Does anyone have an UNIX version of Authorin?  I am looking for a way
> to submit DNA sequence data into genbank from a SUN or UNIX workstation.
> Is there a procedure or program capable of doing this?
> 
> Thank you,
> 
> David Ow
> Human Genome Center, L-452
> Lawrence Livermore National Lab
> 7000 East Ave. Livermore, CA 94550
> email: ow@llnl.gov (ow@tornak.llnl.gov)
> phone: (510) 423-8062  fax: (510) 422-2282
> 

A UNIX version of Authorin was not produced under the previous GenBank
contract.  I believe that NCBI will produce a data submission program
that will run on UNIX platforms sometime in the future.

				Sincerely,

				Dave Kristofferson
				BIOSCI/bionet Manager

				kristoff@net.bio.net
Newsgroups: bionet.molbio.genbank
From: lipman@void.nlm.nih.gov (David Lipman)
Subject: Apologies for Disappearing Division
Organization: National Library of Medicine
X-Newsreader: Tin 1.1 PL4
Date: Tue, 15 Dec 92 16:59:28 GMT

In NCBI/GenBank Release 74.0, there is one new division for EST's, and
two divisions disappeared - the NLM and organelle divisions.  In the
release notes for 73.1 we announced the EST and NLM changes but not the
disappearance of the organelle division.  That omission was unintended
and a mistake for which we apologize.  We understand how frustrating
such surprises can be and we'll do whatever it takes to prevent 
unannounced changes in the flatfile.  In addition, we will announce
any planned changes in the flatfile at least 2 releases in advance
(4 months).  There are no changes planned for the February release
(Release 75.0).

Again, we apologize for any inconvenience.

David Lipman
NCBI/NLM
From: jones@bsm.bioc.ucl.ac.uk (David Jones)
Newsgroups: bionet.molbio.proteins
Subject: Re: Jones, Thorton & Taylor Mutation Data Matrices
Date: 19 Dec 92 00:41:54 GMT
Organization: University College London Biochemistry Dept.

My apologies to the people who have been trying to contact me via
e-mail today. We've been trying out a new e-mail setup, and by
some freak combination of events my e-mail aliases got messed up.
I thought my mailbox was unusually quiet today...

Just to confirm - the address jones@bsm.bioc.ucl.ac.uk is my correct
(and now fully functional) e-mail address.

David Jones
Dept. of Biochemistry and Molecular Biology
University College
Gower Street
London
WC1E 6BT
Tel. 071 387 7050 x3879
From: friedman@mbcl.rutgers.edu
Newsgroups: bionet.molbio.proteins
Subject: Transcription factor with 2 activation sites???
Date: 16 Dec 92 02:53:22 GMT

I am wondering if anyone has heard of a transcription factor which has two
activation sites.  I am trying to find out if a factor which binds to an
enhancer sequence, has the ability to stimulate expression from two promoters,
simultaneously.  I think that this would require that the factor would have to
have two activation sites.  If you any info, please e-mail me .

Thanks
Rich
Friedman@mbcl.rutgers.edu
From: mangalam@SALK-SC2.SDSC.EDU (Harry Mangalam)
Newsgroups: bionet.molbio.proteins
Subject: Re: Transcription factor with 2 activation sites???
Date: 18 Dec 92 18:13:20 GMT
Distribution: bionet

Rich Friedman writes:

>I am wondering if anyone has heard of a transcription factor which has two
>activation sites.  I am trying to find out if a factor which binds to an
>enhancer sequence, has the ability to stimulate expression from two promoters,
>simultaneously.  I think that this would require that the factor would have to
>have two activation sites.  If you any info, please e-mail me .

   There are some transcription factors (TFs) that have multiple DNA
binding domains - Mike Levine's lab characterized one (the name escapes me
at the moment but I could look it up) that had both a "paired" box and a
homeobox (homoeobox for the Brits) and both could bind to completely
different (although in their original work, overlapping) sites.  Recently,
TFs have been cloned which have large numbers of Zn fingers (>15), many of
which seem to be capable of binding DNA, and also recently someone cloned a
monster that had multiple homeoboxes AND multiple Zn fingers.
   If your question is whether a TF with only one DNA binding site can
activate multiple genes, then the answer is also yes, with examples too
numerous to cover.  A favorite example is the anterior pituitary-specific
Pit1 (aka (if inaccurately) as GHF1) which can activate transcription from
both the Prolactin promoter (and in fact is absolutely required for PRL
expression), Growth Hormone promoter (less tightly regulated than PRL), and
TSH gene, as well as its own promoter (all anterior pituitary-specific
genes).

Hope this is of some help
Cheers,
Harry

Harry Mangalam                                   Vox:(619) 453-4100, x250
Dept of Biocomputing                                   Fax:(619) 552-1546
The Salk Institute                        1'   mangalam@salk-sc2.sdsc.edu
10010 N Torrey Pines Rd                   2'        hjm@salk-sgi.sdsc.edu
La Jolla CA 92037                         3'         mangalam@salk.bitnet
Newsgroups: bionet.molbio.proteins
Subject: Re: Transcription factor with 2 activation sites??? (fwd)
From: robison1@husc10.harvard.edu (Keith Robison)
Date: 19 Dec 92 17:06:47 GMT
Distribution: bionet

ghj@mrc-lmb.cam.ac.uk (Jacobs "G.") writes:

>Just to add to the confusion, at least some of the DNA proteins with
>more than one DNA binding domain can select between them via alt.
>splicing. This could appear as activating at two different sites in
>some assays I guess (I'm not an experimentalist, but it does seem an
>obvious point...).
>I could give you some examples later (I'm not at my lab. at the 
>moment).

The Kafatos lab published a pair of papers on this in a recent Science
(about 1 month ago?)

>A point for myself is to distinguish between whether the protein binds
>the two promoters *AT THE SAME TIME* or whether it is able to bind
>the two promoters, but independently. Two very different things!

>Grant Jacobs
>MRC Laboratory of Molecular Biology
>Hillls Road 
>Cambridge CB3 9EU
>ENGLAND.


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

robison@biosun.harvard.edu
From: jones@bsmsol1.ucl.ac.uk (David Jones)
Newsgroups: bionet.molbio.proteins
Subject: Re: Amino Acid Relationships (long)
Date: 17 Dec 92 21:26:46 GMT
Distribution: bionet
Organization: University College London Biochemistry Department

As a follow-up to Harry Mangalam's summary of methods  for representing amino
acid  similarities,  people  might also be  interested in  the following  two
references (one in press, one in print):

The first  paper is something  of a sequel to  Willie Taylor's original  Venn
diagram paper from 1986...

Taylor, W.R., Jones, D.T.
"Deriving an Amino Acid Distance Matrix."
J. Theor. Biol. in press. (1993)

ABSTRACT

Various methods were investigated  to convert an amino acid similarity matrix
into a low-dimensional, metric distance matrix.  Using projection techniques,
no  unique  transformation  was   found  and  of  the  many  inversion  forms
investigated, simple negation normalised by the diagonal  elements produced a
good fit to the original data. An  inter-row distance also gave a  comparable
fit and  when evaluated by weighted  least-squares minimisation  was found to
be  preferable. A  rank-ordered form  of  the matrices  was also  derived  by
constraining  neighbours to  be  equidistant in  (3)  space. This  produced a
network configuration  not unlike  that produced  in a  previous analysis  of
amino  acid  physico-chemical  properties.  The  derived   forms  might  find
applications in  sequence alignment,  including pattern matching  algorithms,
and the construction of phylogenetic trees.


The other reference is...

Taylor, W.R.
"A template based method of pattern matching in protein sequences."
Prog. Biophys. Mol. Biol. 54:159-252 (1989) (published in 1991).

This paper  contains possibly the oldest  reference in  any molecular biology
paper: Wan,  "The I  Ching", privately published  (1142 BC).  If you want  to
know  what Gray codes,  the I  Ching, and  the genetic  code have to  do with
representing amino acid similarities, then this is the paper for you!

---
David Jones
Biomolecular Structure and Modelling Unit
University College London
Newsgroups: bionet.molbio.proteins
From: wrp@cyclops.micr.Virginia.EDU (Bill Pearson)
Subject: Jones, Thorton & Taylor Mutation Data Matrices
Originator: wrp@cyclops.micr.Virginia.EDU
Organization: University of Virginia
Date: Fri, 18 Dec 1992 02:50:07 GMT


	I recall getting some datafiles and programs last May/June that
allowed one to calculate new mutation data matrices based on the data
accumulated by Jones et. al CABIOS (1992) 8:275.  Unfortunately I
cannot find the programs/data now and my mail to jones@bsm.bioc.ucl.ac.uk
is rejected.

	I would greatly appreciate receiving a copy of those programs
and datafiles.

Bill Pearson
From: POSTMASTER@NBRF.GEORGETOWN.EDU
Newsgroups: bionet.molbio.proteins
Subject: Announcement of PIR Service Interruption
Date: 17 Dec 92 15:12:54 GMT
Distribution: bionet


            Announcement of Temporary Interruption of Access to
                   The Protein Identification Resource

The National Biomedical Research Foundation will be attempting to repair a
hardware problem on Monday 21 December.  From 10:00 EST Monday 21 December
through about 12:00 EST Tuesday 22 December it will not be possible for users
to access either the Protein Identification Resource Network Server or the
On-line System.

We regret any inconvenience this temporary loss of service will cause.
------------------------------------------------------------------------
                                 Dr. John S. Garavelli
                                 Database Coordinator
                                 Protein Information Resource
                                 National Biomedical Research Foundation
                                 Washington, DC  20007
                                 POSTMAST@GUNBRF.BITNET
                                 POSTMASTER@NBRF.GEORGETOWN.EDU