HDTenEightyP/NetNews huggingface dataset:
From: GenBank-Updates@genbank.bio.net
Newsgroups: bionet.molbio.genbank.updates
Subject: Human immunodeficiency virus type 1, viral sample LC02.DA18, V3
Date: 7 Apr 92 10:04:58 GMT
Distribution: bionet
Checksum: 48994     3

LOCUS       HIVFLQ618     320 bp ss-RNA             VRL       07-APR-1992
DEFINITION  Human immunodeficiency virus type 1, viral sample LC02.DA18, V3
            region.
ACCESSION   M90921
KEYWORDS    .
SOURCE      Human immunodeficiency virus type 1 (HIV-1), M13 clone DA18 of DNA
            ID 5242.
  ORGANISM  Human immunodeficiency virus type 1
            Viridae; ss-RNA enveloped viruses; Positive strand RNA virus;
            Retroviridae; Lentivirinae.
REFERENCE   1  (bases 1 to 320)
  AUTHORS   Ou,C.Y., Ciesielski,C.A., Myers,G., Bandea,C.I., Luo,C.C.,
            Korber,B.T., Mullins,J.I., Schochetman,G., Berkelman,R.L.,
            Economou,A.N., Witte,J.J., Furman,L.J., Satten,G.A., Curran,J.W.
            and Jaffe,H.W.
  TITLE     Molecular Epidemiology of HIV Transmission in a Dental Practice
  JOURNAL   Science (1992) In press
  STANDARD  full automatic
COMMENT     Kindly submitted in computer readable form by the CDC (Centers for
            Disease Control), Atlanta, GA.
            The sequence in this entry is one of 6 clone sequences over the V3
            region obtained by the CDC from this Florida control sample.
            Please note that for this set of sequences, clone numbers from the
            V3 region do not correspond with similar numbers from the V4C3V5
            region.
FEATURES             Location/Qualifiers
     CDS             <1..>320
                     /note="env polyprotein (AA at 1)"
                     /codon_start=1
                     /translation="LAEEEIVIRSANFTDNTKIIIVQLNESVEINCTRPSNNTRKSIP
                     IGPGRAFYATGDVIGDIRQAHCNISGAKWNNTLKRIVIKLKEQFPNKTIVFNQSSGGD
                     PEIV"
BASE COUNT      141 a     48 c     57 g     74 t
ORIGIN      near the C2-V3 boundary
        1 ctagcagaag aagagatagt aattagatct gccaatttca cagacaatac taaaatcata
       61 atagtacagc tgaatgagtc tgtagaaatt aattgtacaa gacccagcaa caatacaaga
      121 aaaagtatac ctataggacc aggcagagca ttttatgcaa caggagatgt aataggagat
      181 ataagacaag cacattgtaa cattagtgga gcaaaatgga ataacacttt aaaacggata
      241 gttataaaat taaaagaaca atttccaaat aaaacaatag tctttaatca atcctcagga
      301 ggggacccag aaattgtaat
//
From: geojohn@casbah.acns.nwu.edu (George Johnson)
Newsgroups: bionet.molbio.genbank
Subject: Names in records
Date: 16 Apr 92 03:41:20 GMT
Distribution: usa
Organization: Northwestern University, Evanston Illinois.

One problem we have with using Genbank is with multiple
files from one journal article.  Most of the time, the
sequences reported do not have names along with them.
Sometimes we can decifer the name from the clone name
given, but most of the time, we must look through the
entered sequence, trying to reference the published sequence
with the entered one.
I'm sure this has been talked about before, but why does
Genbank not include the published sequence name?
If needed, I can provide specific examples of this.

Thank You,
George Johnson.
From: pgil@HISTONE.LANL.GOV (Paul Gilna)
Newsgroups: bionet.molbio.genbank
Subject: Re: on vector checking
Date: 16 Apr 92 22:28:20 GMT
Distribution: bionet


Bruce,

I have no desire to keep this in-house, particularly as there's nothing
in there that is not already in the full release of GenBank--we are
simply proposing we present a searchable "view" of the database that is
targeted towards vector data. Presenting it for FTP download or even
server retrieval should be no problem.

If folks have their favourite vector sequence that is not available in
either GenBank or the other vector collections--please send it
along--we'd be happy to include it. If you know of glaring absences,
we'll try to come up with the data (and yes, I know about gt11!)


--paul
Xref: sparky bionet.molbio.genbank:276 bionet.info-theory:431
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.molbio.genbank,bionet.info-theory
Subject: Re: Author errors and omissions.
Date: 17 Apr 92 01:28:33 GMT
Followup-To: bionet.molbio.genbank
Distribution: bionet
Organization: NCI Supercomputer Facility, Frederick, MD

In article <robison1.703430730@husc10> robison1@husc10.harvard.edu (Keith Robison)
writes:

>	Do all GAL4 sites share a common motif?

Just doing the 14 ones I know about from GenBank, they have a 14 bit site.
There are not enough examples in this set to determine if there are several
different kinds of motif.

>>       A transcription start site is the nucleotide(s) that represent 
>>       the 5' end of transcribed RNA (precursor).
>
>	See above.

See

@article{Penotti1990,
author = "F. E. Penotti",
title = "Human {DNA TATA} Boxes and Transcription Initiation Sites:
A Statistical Study",
journal = "J. Mol. Biol.",
volume = "213",
pages = "37-52",
year = "1990"}

>>       Signal peptides are amino acid sequences at the N-terminus of a
>>       polypeptide that are cleaved when the protein reaches the ER.
>
>	What amino acid motifs are in signal peptides?
>	Are there conserved motifs around cleavage sites?
>	Are transit peptides annotated as signal peptides (or vice versa
>	i.e., are there chloroplast enzymes marked with signal peptides
>	or secretory proteins annotated with transit peptides)?

I have not attempted an analysis.  Are there enough data in GenBank?
Note that you have to have 5 times as much sequence data for proteins 
(versus DNA) because of the small sample error problem.  You'd probably
need 50 to 100 examples to begin not to be fooled.

>No, no, no!  What I am saying is that if you have a site
>annotated, then it should be checked against the consensus for that
>site.

No Keith, check it against the sequence logo, or a negative log of frequency
weight matrix if you want automation.  Don't get into trouble by using a
consensus.

>The best curator for any sequence is the original author, and the best
>time is when it is submitted!

Right, but newly discovered sites, which are not in a sequence paper are
probably being lost.  Curators need to find these also.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: danj@WELCHGATE.WELCH.JHU.EDU (Dan Jacobson x-8453)
Newsgroups: bionet.molbio.genbank
Subject: * On Vector Checking
Date: 16 Apr 92 20:42:50 GMT
Distribution: bionet


Paul Gilna writes:

>	One thought we have had which we can implement fairly quickly here is
>	to set up a specific FASTA/(BLAST?) searchable file on the GOS that
>	would contain only vector sequence data, allowing the similarity search
>	servers to act as specific checks for vector sequences. We would
>	maintain the file and add any new vectors as they came along.
>	
>	At this point the searchable file contains about 445 sequences from
>	GenBank, including lambda. Chances are there is some redundancy here
>	that could be cured to make the utility even more worthwhile, but we
>	would like to try it out, so that we can get a clearer idea of the work
>	that might be required to winnow out sibling sequences.
>	
>	We would appreciate some feedback on its usefulness and any suggestions
>	for improvement will be entertained.


Yes, Yes, Yes (as Keith would say) - In addition can this file be the foundation
for a vector database?  VECTOR which comes with GCG is a dead database as it's creators gave it up some years ago in the hope that genbank (or somebody) would take over such a project, as such is is hopelessly out of date.  I've heard
many a question on the bionet groups of the type - "does anybody have the sequence for vector X I can't find it anywhere and ......" .  I've also heard
the same type of requests in the labs here so that it would seem that there is a
need. 

Sincerely,

Dan Jacobson

danj@welchgate.welch.jhu.edu
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.molbio.genbank
Subject: Re: Author errors and omissions.
Date: 17 Apr 92 17:08:05 GMT
Distribution: bionet
Organization: NCI Supercomputer Facility, Frederick, MD

In article <1992Apr17.063108.9610@ncsu.edu> samodena@csemail.cropsci.ncsu.edu
(S. A. Modena) writes:

>I personally do not doubt that databases full of lurking errors will be
>the down fall of many a "scientist," because in the end the career push
>will lead many to publish garbage and then move to outright fraud when one
>can no longer stand to struggle with corrupted resources.

The garbage I can attest to already.  The fraud in this field I have yet to
see.  Hmm.  Yes, GenBank is a corrupted resource.  Nice accurate phrase, even
if it is a bit nasty.

>I see no grand investment opportunity in building new software or new
>software methodologies to support the genome projects or mol bio in general
>because the "beneficiaries" don't sound like they are interested in
>making a monetary, high-risk investment in what it's really going to take
>to save your asses down the road.
>
>Turn the sequencing machines on and let'er rip.  Produce tons of exciting
>"new" DNA sequences as fast as you can and maybe no one will notice that
>it's pure hack.  Patent a few of them: they'll be worth a fortune someday
>when someone tries to "use" them.

Gosh I hate it when I agree with you and you are in a bad mood!  :-)

I don't think sending money to GenBank will solve the problem.  It has to come
from an awareness by every molecular biologist that the data in GenBank are
their responsibility and their legacy.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
From: ABOLA@PB3.PDB.BNL.GOV
Newsgroups: bionet.molbio.genbank
Subject: Protein Data Bank ftp server
Date: 9 Apr 92 02:25:57 GMT
Article-I.D.: PB3.920408222557.402
Distribution: bionet

The PDB has an e-mail file server available for your use. This server provides
PDB general information and documentation files. For more information, send an
e-mail message to fileserv@pb1.pdb.bnl.gov and include the following text:

	send info your_e-mail_address.

The PDB has an anonymous FTP account available on the system pdb.pdb.bnl.gov
with Internet address 130.199.144.1. It is possible to transfer files to and
from this system using anonymous as the FTP user name and your real user name
as the password. PDB general information and documentation files, as well as
pre-release atomic coordinate entries, are available for downloading. You also
can upload any files that you may wish to send to the PDB. Those using VMS may
need to place quotes around file names. 

Anyone experiencing problems or having questions related to the above network
services is requested to send an e-mail message to skora@bnl.gov.
From: kristoff@genbank.bio.net (David Kristofferson)
Newsgroups: bionet.molbio.genbank
Subject: Re: Author errors and omissions.
Date: 17 Apr 92 17:14:28 GMT
Distribution: bionet
Organization: GenBank Online Service

> Everytime someone says: that's easy; it can be done with a simple little
> program....I know I'm talking to someone who is an UNprofessional programmer.

We were just discussing in-house the other day that this has often
been the initial attitude that people take about Authorin development.

8-)

Dave "thousand points of light" Kristofferson
From: kristoff@GENBANK.BIO.NET (Dave Kristofferson)
Newsgroups: bionet.molbio.genbank
Subject: Floppy Release 71 (FINAL ONE!!) ready for FTP
Date: 10 Apr 92 23:18:45 GMT
Distribution: bionet


The 


			      ***last***
				 ====


release of GenBank binary files (usually referred to as the "floppy
disk format") is now available for FTP from genbank.bio.net
[134.172.1.160] in pub/db/gb-floppy.  These binary files are produced
from the GenBank version 71 flat file release.

Data files are in pub/db/gb-floppy/data and IBM PC programs are in
pub/db/gb-floppy/pc.  The release notes will be added to
pub/db/gb-floppy when ready.

All files must be FTPed in **binary** mode.

The growth of the database came *very* close to bursting the limits of
this format (only 2-3 more days worth of new entries would have
necessitated omitting data to produce the files!!).  In one case (the
index of accession numbers) a format limitation was encountered.  For
this last release, only *primary* accession numbers are included in
the accession number index.

If you have software which requires this binary data format, please
contact your supplier regarding their plans for future updates.  It is
likely that you will require a software upgrade to handle the newer
formats which will be produced by NCBI later this year.

For GenBank CDROM and floppy disk subscribers, the masters are going
to the duplicators today, and I expect that we will begin shipping
late next week or early on the following week.

IntelliGenetics will produce two more ASCII flat file releases of
GenBank (#s 72 and 73) in June and September respectively.  One more
release of GenPept will be produced in June, but GenPept daily updates
will continue on GOS up through 30 September.

The release 72 and 73 CDROMs will include the following:

Rel. 72 CDROM:	GenBank flat file release 72
		GenPept flat file release 72
		GenBank floppy release 71 (repeat of the current release)

Rel. 73 CDROM:	GenBank flat file release 73
		GenBank floppy release 71 (repeat of the current release)

Enjoy!  I was given the facetious suggestion of labeling the final
CDROM "GenBank's Greatest Hits!"  I will give this some serious
consideration.

				Sincerely,

				David Kristofferson, Ph.D.
				GenBank Manager

				415-962-7339

				kristoff@genbank.bio.net

Newsgroups: bionet.molbio.genbank
From: reisner@ee.su.oz.au ()
Subject: CD-ROM discs from GenBank
Reply-To: reisner@ee.su.oz.au ()
Organization: Electrical Engineering, The University of Sydney, Australia
Distribution: bionet
Date: Mon, 6 Apr 1992 22:55:55 GMT


Ross Smith writes:

>We have a number of ideas for dealing with this, but before exposing our
>ignorance we would be keen to hear how others (VAX/VMS or otherwise) plan
>to deal with this 'forced' change to the CD-ROMs.
======================================================

While we run a Sun shop and have CD-ROMs in place which are mountable by the
Sun's,  we also have a US$550 CD-ROM drive from apple.  The Mac it is
attached to is connected to the network via ethernet and the software
supplied with the Apple drive 'sees' iso 9660 formatted discs.  We have no
trouble ftping the files from the EMBL disc to the Sun server from the Mac
using either Fetch or the ftp facility in PacerTerm, but as binary files,
not text.   The equivalant approach would be at least as easy with PC's.

In our set up we move 25-30 Kbytes/second.

Alex Reisner
From: pgil@HISTONE.LANL.GOV (Paul Gilna)
Newsgroups: bionet.molbio.genbank
Subject: Re: Author errors and omissions.
Date: 16 Apr 92 02:38:32 GMT
Distribution: bionet

> Just so there is no misunderstanding, I am not blaming the current GenBank 
> staff for the problems in the database. Despite it's flaws, it is wonderful 
> compared to what it was like with a previous contractor. I think the blame 
> should go to the NIH who lets the GenBank contract. If they specified that 
> the quality of the annotation should be improved on the old loci, then 
> something might happen. Perhaps if the muckamucks at the NIH knew how 
> people felt about this they might try to do something about it.
> 
> Just my two cents worth.
> 
> 
> Steve Clark
> 
> clark@salk-sc2.sdsc.edu  (Internet)
> clark@salk               (Bitnet)


I have to admit, Steve, that I take exception to the above. it appears to
imply that those working in the GenBank contract do little else than
serve to appease the contractual deities at NIH, by doing only what we
are told to do.

With all due respect to the folks at NIH, the fact that GenBank is
where it is today has a lot more to do with the vision, planning and
commitment of the folks here at LANL and at IG than can be expressed in
mere contractual guidelines.

Fundamental and far-reaching changes have been made with this project
that have brought lasting improvement to the service obtained by the
community, because a bunch of people had the guts and the belief in
themselves and their co-workers to commit their careers to that
project.

Of course we are not perfect, of course we have a long way to go, but
the momentum that has brought us this far has not abated, NIH or no
NIH, the quality of annotation WILL improve.

Steve, why not be part of the solution? Sign on as a curator, and come
help us all.


--paul
From: smith@mcclb0.med.nyu.edu
Newsgroups: bionet.molbio.genbank
Subject: NCBI wants to discontinue VAX/VMS GenBank tapes....
Date: 6 Apr 92 19:20:28 GMT
Organization: NYU Medical Center, New York, NY 10016, USA

I just got a letter from Dennis Benson, Chief of the Information Resources 
Branch of NCBI saying that NCBI wants to discontinue the VAX/VMS 6250bpi
backup tape GenBank distribution, and replace it with a CD-ROM distribution.

The price will be <$60 for bi-monthly updates for a year of the CD-ROM (sounds
good!) vs. $700-$1,000 for the tapes for a year (lousy deal).

Despite the very attractive price of the CD_ROM version, it is not clear that 
this will really be usefull to us: not the least of the problems is that 
VAXes, ours anyway, does not have CD-ROM and even if we did it would not (yet) 
read ISO 9660.

We have a number of ideas for dealing with this, but before exposing our 
ignorance we would be keen to hear how others (VAX/VMS or otherwise) plan
to deal with this 'forced' change to the CD-ROMs.

+----------------------------------------------------------------------------+
|Ross Smith,  Research Computing Resource, Department of Cell Biology, NYU-MC|
|550 First Ave., NYC, 10016-6402.  Phone: (212) 263-5356: FAX: (212) 263-8139|
|E-Mail:  SMITH@NYUMED.BITNET (BITNET),   SMITH@MCCLB0.MED.NYU.EDU (Internet)|
+----------------------------------------------------------------------------+
Newsgroups: bionet.molbio.genbank
Subject: Re: CD-ROM discs from GenBank
From: bioc06@otago.ac.nz
Date: 8 Apr 92 15:25:46 +1300
Distribution: bionet
Organization: University of Otago, Dunedin, New Zealand

In article <1992Apr6.225555.23870@ucc.su.OZ.AU>, reisner@ee.su.oz.au () writes:
> 
> Ross Smith writes:
> 
>>We have a number of ideas for dealing with this, but before exposing our
>>ignorance we would be keen to hear how others (VAX/VMS or otherwise) plan
>>to deal with this 'forced' change to the CD-ROMs.
> ======================================================
> 
> While we run a Sun shop and have CD-ROMs in place which are mountable by the
> Sun's,  we also have a US$550 CD-ROM drive from apple.  The Mac it is
> attached to is connected to the network via ethernet and the software
> supplied with the Apple drive 'sees' iso 9660 formatted discs.  We have no
> trouble ftping the files from the EMBL disc to the Sun server from the Mac
> using either Fetch or the ftp facility in PacerTerm, but as binary files,
> not text.   The equivalant approach would be at least as easy with PC's.
> 
> In our set up we move 25-30 Kbytes/second.
> 
> Alex Reisner

I missed the initial posting of this, but I can comment on the difficulty of
reading ISO 9660 CD-Roms under VMS.  The answer is that VMS does not support
ISO 9660, nor could I discern any immediate intention to correct this glaring
omission.

I have written a utility (CD_ACCESS) which is available from the EMBL server,
or if necessary from here which allows file transfer from CD-roms under VMS.
Clearly this is only a partial solution since it does not really allow the
database to appear on line to normal VMS/RMS, thus freeing up many megabytes of
disk.  However, if needs must...

Peter A. Stockwell
From: doelz@comp.bioz.unibas.ch (Reinhard Doelz)
Newsgroups: bionet.molbio.genbank
Subject: Re: on vector checking
Date: 17 Apr 92 08:28:36 GMT
Reply-To: doelz@urz.unibas.ch
Distribution: bionet
Organization: EMBnet Switzerland [BASEL]

In article <16APR199216563581@aardvark.ucs.uoknor.edu>, broe@aardvark.ucs.uoknor.edu (Bruce Roe) writes:
|> 	How's about putting this database of vector sequences
|> someplace where we could obtain it via ftp and maybe even in
|> the GCG or other popular format?   VecBase, as Dan J. said in
|> a subsequent posting is very out of date.  Please don't just

The best would be a generally accepted flat file format. 
I could make PIR/GCG available on bioftp if needed. 

-- 
+----------------------------------+-------------------------------------+
|    Dr. Reinhard Doelz            | RFC     doelz@urz.unibas.ch         |
|      Biocomputing                | DECNET  20579::48130::doelz         |
|Biozentrum der Universitaet       | X25     022846211142051::embnet     |
|   Klingelbergstrasse 70          | FAX     x41 61 261- 6760 or 2078    | 
|     CH 4056 Basel                | TEL     x41 61 267- 2076 or 2247    |   
+------------- bioftp.unibas.ch is the SWISS EMBnet node ----------------+
               -----------------------------------------
From: goldman@mbcl.rutgers.edu
Newsgroups: bionet.molbio.genbank
Subject: Re: CD-ROM from Genbank: further comments
Date: 8 Apr 92 12:35:02 GMT
Distribution: bionet

In article <199204080502.AA09029@Menudo.UH.EDU>, Davison@UH.EDU (Dan Davison) writes:
> In addition to Peter Stockwell's (bioc06@otago.ac.nz) excellent
> CD ROM drivers for VMS (CD_ACCESS) there is also the US Geophysical
> Survey PD drivers; I got them quite a while ago from someone at JPL
> and from the file below I assume it's on a DECUS tape (or ironically,
> CD) somewhere. 
> 
> They are functionally the same as Dr. Stockwell's; which to use is
> probably dependent on your system manager (CD_ACCESS is easier to set
> up). 
> 
> My discussions with DEC both in Houston and Marlboro (?) indicated
> that ISO 9660 as-native-file-sytem was low priority, and might appear
> as early as VMS 5.6 (later this year 3Q 92?) but more likely "a year
> away". We all know what DEC means when they say that...
That's kind of distressing.  I thought it was closer than that (i.e definite
for 5.6).

> 
> Also, from painful experience, I would *forget* the $250 driver from
> DEC. Unless you enjoy FDL and deep RMS munging, that it.
Yeah, that was my impression too.  However, the documentation for this  driver
kind of implies that if appropriate XARs  are written on the CD-ROM, then
everything is hunky-dory & you can read  the CD-ROMs no problem.  Is this true?
- has anyone seen such a CD-ROM?  If it were true, and if it didn't influence
other people's ability to read them, could NCBI write the XARs onto the CD-ROM? 
Dennis Benson, please come in.

			Adrian

-- 
Adrian Goldman                         |  Internet:  Goldman@MBCL.Rutgers.Edu
Molecular Biology Computing Laboratory |  Bitnet:    Goldman@BioVAX
Waksman Insitute,                      |  Phone:     (908) 932-4864
Rutgers University,                    |  Fax:       (908) 932-5735
Piscataway, NJ 08855 USA               |