From owner-recombination@net.bio.net Sun Oct 03 15:19:00 1999
Path: biosci!biosci!not-for-mail
From: "Dr. Mark Chance" <mrc@aecom.yu.edu>
Newsgroups: bionet.molbio.recombination
Subject: Research Scientist Position
Date: 3 Oct 1999 09:19:40 -0700
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----------------------------------------------------------
Mark R. Chance, Albert Einstein College of Medicine
Center for Synchrotron Biosciences, An NIH Shared
 Resource
 Ullman 315, Department of Physiology & Biophysics
 1300 Morris Park Ave., Bronx NY 10461
 ph. 718-430-4136; fax-718-430-8587; internet :
 mrc@aecom.yu.edu
 http://beam.aecom.yu.edu/Phys&bio/csb1.htm
 
 *********************************************
 Mark R. Chance,  Professor of Physiology &
 Biophysics and Biochemistry 
 and Director, Albert Einstein Center for 
 Synchrotron Biosciences, An NIH Resource Center
 Albert Einstein College of Medicine
 Ullmann 315, Department of Physiology & Biophysics
 1300 Morris Park Ave., Bronx NY 10461
 ph. 718-430-4136; fax-718-430-8587; internet :
 mrc@aecom.yu.edu
 http://beam.aecom.yu.edu/Phys&bio/csb1.htm
 Also
 National Synchrotron Light Source, Brookhaven
 National Labs
 Building 725A-X9
 Upton NY 11973
 ph: 516-344-3800; fax-516-344-5594
 *********************************************
 
 


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From owner-recombination@net.bio.net Tue Oct 12 19:16:00 1999
Path: biosci!biosci!not-for-mail
From: eveljkve@ubbg.etf.bg.ac.yu (Veljko Veljkovic)
Newsgroups: bionet.molbio.recombination
Subject: HIV recombination and dangers of AIDS
Date: 12 Oct 1999 13:16:44 -0700
Organization: MRC Human Genome Mapping Project
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Dear Colleges, 
For most researchers working on the AIDS problem it is
clear that HIV represents a necessary but not
sufficient condition for AIDS. This is             
the reason why it is harmful to reject it as a
causative agent of AIDS.
                
But also it is not less harmful to accept the current
rigid and
                oversimplified view on its role in
AIDS, which resulted in a wrong and
                dangerous therapy and irreparable loss
of precious time in fight with
                the AIDS epidemic. 

                I would like to draw your attention to
another important aspect of this
                problem. According to our decade long
research a significant factor in
                AIDS pathogenesis represents a
recombination between HIV and
                coinfecting  pathogens, endogenous
retroviruses, as well as the host
                genes. This process allows HIV to
evolve fast, resulting in avoidance
                of
                an effective immune response and the
multypathway  attack on the host
                immune and neuronal system. The key
player in this game is the gene
                encoding HIV envelope glycoprotein
gp120. Unfortunately, existing
                genotoxic therapy stimulates this
process and as result of this therapy
                we have today in circulation new
resistant and more aggressive HIV
                strains. What is even worse, existing
AIDS vaccine candidates are based
                on the viral vectors carrying the
HIV-1 envelope gen. Viruses modified
                in this way represent possible prone
for recombination with the endemic
                pathogens which could result in
generation of a new chimeric pathogens
                (currently hundreds of people in
Uganda are vaccinated with
                the canarypox virus carrying the
recombinogenic HIV-1 gp120 
                gene with risk of new epidemic
initiated by recombination between the
                vaccine vector and the endemic viruses
(Ebola, monkeypox and Marborg).
                In three papers which we have
published this year in the peer-reviewed
                journals we have strongly confirmed
this possibility demonstrating that
                (1) HIV can recombine in vivo with
coinfecting bacteria forming
                chimeric
                quasispecies, and (2) that normal
HIV-negative sera contains antibodies
                reacting with principal neutralizing
antigenic region within HIV-1 V3
                loop. 

                It is absurd that people should be
alarmed about genetically modified
                food and that nobody should pay any
attention to the vaccination of
                thousands people with recombinant
viral vectors carrying the most
                dangerous HIV component representing a
potential source of new
                infectious diseases with unpredictable
influence on the human
                population. 

                I am enclosing my letter concerning
this problem which I have sent to
                WHO and NIH a year ago. More details
about the AIDS vaccine problem, as
                well as my nearly decade long
correspondence with the key people from
                WHO and NIH containing arguments from
both sides concerning this
                problem
                can be found on the Internet address
www.newstrolls.com.

                I am inviting all colleges to
contribute by "pro at contra" 
                arguments to the solution of this
important problem.

                Veljko Veljkovic 



                References

                1.. Prljic J., Veljkovic N., Doliana
R., Colombatti A., Johnson E.,
                Metlas R., Veljkovic V. Identification
of an complete and active
                recombinational hot spot within the
HIV-1 gp120 gene: possible
                implications for the AIDS vaccine
development. Vaccine,  Vol. 17, 1462
                (1999).

                2. Metlas R., Trajkovic D., Srdic T.,
Veljkovic V., Colombatti A. Human
                immunodeficency virus V3
peptide-reactive antibodies are present in
                normal HIV-negative sera. AIDS Res.
Hum. Retrovir., Vol. 15, 671
                (1999). 

                3. Metlas R., Trajkovic D. Srdic T.,
Veljkovic V. Colombatti A. Anti-V3
                and anti-IgG antibodies of healthy
individuals Share complementarity
                structurers.  J. Acquir. Immune.
Defic. Sindr., Vol. 21, 266 (1999).




                The WHO/NIH letter

                Dr. Hirosi Nakajima Dr. Harold Varmus
                Director general NIH Director
                Headquarters Office Office of the
Director
                World Health Organisation National
Institutes of Health (NIH)
                Avenue Appia 20 Bethesda, Maryland
20802
                1211 Geneva 27

                October 16, 1998

                Dear Dr. Nakajima/Varmus,

                The CDC announced on October 6, 1998,
that new drugs helped reduced the
                number of AIDS deaths by 47 percent
last year in the US, dropping the
                disease from the 10 leading causes of
death. The information concerning
                this transient success, transmitted by
the press agencies worldwide,
                could erroneously lead to the wrong
conclusion that we are close to
                controlling AIDS, transforming it from
an acute to a chronic disease. 
                Scientists of course should know that
the reality is completely
                different. In the first half of this
year the following has been 
                reported: (1) the appearance of an
infective HIV-1 variant resistant to
                multiple reverse-transcriptase and
protease inhibitors, in other words
                resistant to all known effective
antiretroviral therapy [Hecht et al.,
                New Engl. J. Med. 339: 307 (1998)],
(2) identification of a new HIV-1
                subtype distinct from other known
subtypes, which escapes detection by
                all currently employed HIV tests
[Simon et al., Nature Med. 4: 1032
                (1998)], (3) the finding that one of
the most promising AIDS vaccine
                candidates prepared for clinical
trials may in fact cause AIDS
                [Ruprecht
                et al., Proc. 12th World AIDS Conf.
1998, Art. 608], and (4) that
                atypical transmission of HIV may
occur, meaning that the virus can
                spread through populations with no
identified risk factor for
                transmission [Belec et al., J. Virol.
72: 5831 (1998)]. Behind all of
                these events, reminding us of the
tragic fact that the 14 year battle
                against AIDS has definitely not been
won, is the evolution of variation
                in HIV. Worse still, the current
development and testing of AIDS
                vaccines appears to accelerate this
unpredictable, uncontrollable and
                thus dangerous process of viral
genetic variation. 

                Seven years ago in our letters to WHO
and NIH, the two most responsible
                organizations for AIDS vaccine
development, we explained the
                potentially
                negative effects of AIDS vaccines
based on the HIV-1 gp120/160,
                suggesting that from both practical
and especially ethical reasons,
                decisions concerning the conduction of
clinical trials of these
                vaccines, should be carefully
reexamined (see enclosed the substantive
                text of this demand which was
published in Vaccine, enclosure 1).
                Possible harmful effects of such an
AIDS vaccine could be summarized as

                follows: (1) it could make vaccinees
more vulnerable to HIV infection,
                and (2) it could generate new
pathogens with unpredictable effects on
                the human immune and neuronal system
(molecular basis of these negative
                effects is given in the enclosed
paper, enclosure 2). Unfortunately,
                key
                people from the WHO and NIH which are
responsible for development of
                AIDS vaccines, although alerted to
this risk, ignored it, often using
                baffeling and scientifically
unacceptable arguments (see the enclosed
                correspondence, enclosure 3). 

                Our recent experiments have confirmed
in vivo recombination between
                HIV-1 and coinfecting bacteria (see
the enclosed article which is in
                print, enclosure 4). These results
confirmed the possibility of
                generation of chimeric pathogens
representing a natural recombination
                between HIV and coinfecting bacterial
and viral pathogens. The recently
                reported spread in the US and
elsewhere of the chimeric form of
                Mycoplasma fermentas carrying the
HIV-1 gp120 gene which has been
                implicated in the Golf war syndrome
[Nicolson at al., Int. J. Medicine,
                1, 80-92 (1998)], definitely confirmed
that chimeric recombination
                between bacteria and HIV can represent
stabile and extremely 
                infectious pathogens which spread very
fast through populations. These
                facts strongly emphasize that, despite
the urgent need for preventive
                AIDS vaccines, it would be wise to
introduce a moratorium on clinical
                trials until there is a serious
reexamination of the current concepts
                for their development. Furthermore,
such vaccines could become the
                source of potentially new infectious
diseases rather than an effective 
                instrument for AIDS prevention.
Unfortunately, researchers worldwide,
                supported by WHO and NIH, despite this
risk continue developing and
                testing AIDS vaccines using as vectors
different very contagious
                viruses
                and bacteria. 

                I hope that the WHO and NIH, as the
two most responsible organizations,
                will seriously reflect on this problem
and consider a moratorium on
                further uncontrolled development and
laboratory testing of recombinant
                viral and bacterial vectors carrying
HIV genes, as well as premature
                clinical testing of AIDS vaccines
which, without complete knowledge of
                the biological and immunological
properties of HIV, could produce 
                irreparable and irreversible long term
consequences. 

                Sincerely yours,

                Veljko Veljkovic

                ---

=====



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From owner-recombination@net.bio.net Tue Oct 12 19:18:00 1999
Path: biosci!biosci!not-for-mail
From: cweil@uidaho.edu (Clifford Weil)
Newsgroups: bionet.molbio.recombination
Subject: Graduate Student Assistantship
Date: 12 Oct 1999 13:18:13 -0700
Organization: BIOSCI International Newsgroups for Molecular Biology
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cweil@uidaho.edu or to :

Clifford Weil
Dept. of Biological Sciences
University of Idaho
Moscow, ID  83844-3051


Clifford Weil
Associate Professor
Dept. of Biological Sciences
Univ. of Idaho
Moscow, ID 83844-3051 USA
Tel: 208-885-6370
Fax: 208-885-7905





=====



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From owner-recombination@net.bio.net Fri Oct 15 07:47:00 1999
Path: biosci!biosci!not-for-mail
From: "Mike Briley"
Newsgroups: bionet.molbio.recombination
Subject: Symposium on Molecular Genetics in Mental
Date: 15 Oct 1999 01:46:58 -0700
Organization: ImagiNET
Lines: 27
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There is still time (just) to register for the
Symposium on Molecular
Genetics in Mental Disorders that will take place in
Castres, France 1-3
December 1999.
Full details (including registration forms) are
available from
http://www.entretiens-du-carla.com

Mike Briley






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From owner-recombination@net.bio.net Fri Oct 15 07:47:00 1999
Path: biosci!biosci!not-for-mail
From: cweil@uidaho.edu (Clifford Weil)
Newsgroups: bionet.molbio.recombination
Subject: Graduate Student Assistantship
Date: 15 Oct 1999 01:46:58 -0700
Organization: BIOSCI International Newsgroups for Molecular Biology
Lines: 46
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Available immediately, one graduate research
assistantship at the University of Idaho, to study DNA
repair in plants.  The project involves using Ac/Ds
transposons and the damage caused when they excise to
look at plant DNA repair of the excision sites (see
Plant J. 12:1419-1428(1997)).

Work will involve use of DNA constructs introduced and
recovered from plant cells to examine DNA damage and
repair during transposon excision and analysis of
Ac/Ds transposition in yeast cells.  The degree is
through the Molecular Biology Dept. graduate program,
and the compensation package starts at $16,100.
                     
Please send letter of interest, CV (including GRE
scores and description of previous lab experience) and
the names of three references, either to

                cweil@uidaho.edu or to :

                Clifford Weil
                Dept. of Biological Sciences
                University of Idaho
                Moscow, ID  83844-3051


                Clifford Weil
                Associate Professor
                Dept. of Biological Sciences
                Univ. of Idaho
                Moscow, ID 83844-3051 USA
                Tel: 208-885-6370
                Fax: 208-885-7905


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From owner-recombination@net.bio.net Fri Oct 15 07:51:00 1999
Path: biosci!biosci!not-for-mail
From: BIOSCI Administrator <biohelp@net.bio.net>
Newsgroups: bionet.molbio.recombination
Subject: BIOSCI/bionet miniFAQ & Fundraiser
Date: 15 Oct 1999 01:51:11 -0700
Organization: BIOSCI International Newsgroups for Molecular Biology
Lines: 389
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(LAST REVISION: 14-AUG-99)

This BIOSCI "miniFAQ" is designed to answer the
questions that come up
the *most frequently*.  The main BIOSCI FAQ
(Frequently Asked
Questions) is accessible on the World Wide Web at URL
http://www.bio.net/.

If you can not find an answer to your question in this
or other
documentation, the BIOSCI technical support staff
answers e-mail
queries sent to

     biosci-help@net.bio.net

We can only answer questions about the use of the
newsgroups and
mailing lists.  We unfortunately do not have the staff
to do Internet
information searches or answer scientific questions. 
Please post
those to the appropriate BIOSCI/bionet newsgroups.


       Contents:
       --------
       0) BIOSCI NEEDS YOUR SUPPORT!!

       1) Using the WWW to access the BIOSCI/bionet
newsgroups.

       2) What to do about "spams," i.e., junk mail,
ads, etc.

       3) Examples of subscribing and unsubscribing to
the mailing lists.

       4) The BIOSCI user address and research
interest directory.


0) BIOSCI NEEDS YOUR SUPPORT!!
------------------------------
BIOSCI's government funding has been expended, and we
are now
operating solely from advertising revenue that we have
raised from our
Web site at http://www.bio.net/.  We need just a few
minutes of your
time to help us serve you.

You can do two important things which will take very
little time for
you individually and will immensely help us continue
to help you.

First, please use our WWW system at
http://www.bio.net/ to access the
archives.  You can post or reply to messages via your
Web browser as
described in item #1 below.  Your usage helps attract
sponsors. If you
contact any of our sponsors, please be sure to thank
them for
supporting BIOSCI. It is critical for them to get this
feedback if
they are to continue their sponsorship for the long
term.

Second, if you work for a company or organization that
provides
products or services of interest to the biology
community, please pass
this message on to your marketing or marketing
communications
department or other appropriate group.  Please ask
them to help
support BIOSCI by sponsoring our Web site and explain
the uses and
benefits of the system to the biology community. If
they are
interested, they can then contact us for further
information at our
tech support address, biosci-help@net.bio.net.


1) Using the WWW to access the BIOSCI/bionet
newsgroups.
--------------------------------------------------------
All BIOSCI/bionet full newsgroups are accessible
through the World
Wide Web (WWW) at URL http://www.bio.net.  One can
read and reply
publicly or privately to both recent postings and
archived messages
through one's Web browser if it is configured properly
to send e-mail.
Each newsgroup is equipped with its own WAIS index. 
The main BIOSCI
home page also has access to the BIO-JOURNALS Table of
Contents
database WAIS index and the BIOSCI user address
database described in
another item further below.


2) What to do about "spams," i.e., junk mail, ads,
etc.
-------------------------------------------------------
BIOSCI is a set of parallel USENET newsgroups (the
"bionet" groups),
mailing lists, and a hypermail archive at URL
http://www.bio.net/.
The same postings are distributed on all media (except
for a small
number of mailing-list-only groups at net.bio.net). 
Unfortunately it
is becoming a despicable practice on the Internet (by
a few people out
to make a fast buck) to do automated mass postings to
thousands of
newsgroups and mailing lists.  These attempts to grab
free advertising
are refered to as "spams" in the usual, somewhat
boneheaded, net
terminology.  USENET is more susceptible to this
practice, and many
spams originate on the USENET groups and then are
passed on to the
mailing lists.  However, spammers also get lists of
mailing addresses
and hit these too, so neither medium is immune.

What should you do personally if you get junk mail?
---------------------------------------------------
Just delete it and move on without reading it further.
 Filing a
protest is becoming increasingly useless because
spammers are often
disguising the addresses where the messages are sent
from.  Unless you
really understand Internet mail systems, your attempt
at protest by
sending replies to the message will often end up being
sent to the
address of an innocent person that the spammer is
victimizing.

What can BIOSCI/bionet do to protect its newsgroups?
----------------------------------------------------
The only solution currently available is to moderate
the newsgroup.
If this newsgroup is already moderated, then you are
in good shape.
Moderation protects the USENET distribution from about
95% of the
spams that are being sent to date and protects the
mailing lists
completely.  Moderation means, however, that someone
has to take the
time to review each message before it goes out.  We
have set up
software here that simply allows the moderator to
forward to an
address at net.bio.net messages that (s)he wishes to
have distributed.
This takes no more time than that needed to read the
message and pass
it on, say about 1 min. per message.

Most newsgroups currently have a discussion leader who
is responsible
for their newsgroup.  The discussions leaders and
their e-mail
addresses are listed in the BIOSCI Information Sheet
which is
available on the Web at http://www.bio.net/.  If a
newsgroup is being
hit with too many junk postings, please contact the
discussion leader
for that group and see if there is interest in
moderating the group.
Please do not assume that by simply posting a
complaint to the
newsgroup itself, anyone on the BIOSCI staff will act
on your
complaint.  With close to 100 newsgroups to run, the
BIOSCI staff has
to rely on the discussion leaders of each newsgroup to
report problems
directly to us at biosci-help@net.bio.net.

We will moderate any of our newsgroups if the
discussion leader tells
us that the readership of the group wishes to do so
and if a moderator
is willing to do the work.  For most BIOSCI/bionet
groups, this
entails only a few minutes of work each day.

Moderating a newsgroup will resolve probably 95% of
the junk postings
on the USENET distribution.  Unfortunately there are
easy ways for
determined spammers to override the moderation
mechanism on USENET,
but we can protect our e-mail subscribers from
unwanted postings if
the newsgroup is moderated.  You can also access our
newsgroups over
the WWW at URL http://www.bio.net.  While this Web
interface will not
stop spammers from trying to post to the groups, this
will give you
yet another way, besides using USENET news, to keep
the junk out of
your personal mail files.  For those of you with local
USENET news
systems, the Web interface will also give you faster
access to new
newsgroups and recent postings.


3) Examples of subscribing and unsubscribing to the
mailing lists.
------------------------------------------------------------------
PLEASE NOTE: The BIOSCI management does NOT act on
subscription/unsubscription requests that are posted
improperly to the
newsgroups and mailing lists.  People who do this only
bother everyone
on the lists to no avail.  Please be sure to follow
the proper
procedures below.

Gory details are in the BIOSCI Information sheets on
the Web at
http://www.bio.net.  Below we give an example
utilizing the
METHODS-AND-REAGENTS list at both of our two BIOSCI
sites:

Users in the Americas and Pacific Rim countries who
use the BIOSCI
------------------------------------------------------------------
node at computer net.bio.net:
----------------------------

A) Determine the "listname" which is the <=8 character
mail address
      ^^^^^^^^^^^^^
  for the group.  These can be found in the BIOSCI
Info. Sheet.  For
  the METHODS-AND-REAGENTS group the mailing address
is
  methods@net.bio.net.  The listname is the portion of
the address to
  the left of the @ sign, i.e., "methods".  The
listname is used with
  the "subscribe" and "unsubscribe" commands
illustrated below.

B) Mail all commands in the body of a mail message
addressed to
  biosci-server@net.bio.net.  Do NOT send commands to
the newsgroup
  posting addresses!  Leave the Subject: line blank,
any text on it
  will be ignored.

C) In the body of your message put one or more of the
following
  commands with an "end" command on the last line,
e.g.,

  subscribe methods
  unsubscribe methods
  end

  Do NOT put your e-mail address or other text on
these lines.  The
  server only allows you to cancel your subscription
if the address
  on your mail header matches the address on our
mailing list.
  Please ask for help at biosci-help@net.bio.net if
your address has
  changed, e.g., if you know you are on the list but
the server tells
  you that you are not a member.


Users in Europe, Africa, and Central Asia who use the
BIOSCI node at
--------------------------------------------------------------------
the UK-HGMP-Resource Centre (known as hgmp.mrc.ac.uk):
-----------------------------------------------------

A) Determine the "listname" which is the <=8 character
mail address
      ^^^^^^^^^^^^^
  for the group.  These can be found in the BIOSCI
Info. Sheet.  For
  the METHODS-AND-REAGENTS group the mailing address
is
  methods@hgmp.mrc.ac.uk.  The listname is the portion
of the address
to
  the left of the @ sign, i.e., "methods".  The
listname is used with
  the "subscribe" and "unsubscribe" commands
illustrated below.

B) Mail all commands in the body of a mail message
addressed to
  majordomo@hgmp.mrc.ac.uk.  Do NOT send commands to
the newsgroup
  posting addresses!  Leave the Subject: line blank,
any text on it
  will be ignored.

C) In the body of your message put one or more of the
following
  commands with an "end" command on the last line,
e.g.,

  subscribe methods
  unsubscribe methods
  end

  Please ask for help at biosci@hgmp.mrc.ac.uk if your
address has
  changed, e.g., if you know you are on the list but
the server tells
  you that you are not a member.


4) The BIOSCI user address and research interest
directory.
-----------------------------------------------------------
Please take this opportunity to add your name,
address, and research
interest information to the BIOSCI User Address
Database if you have
not already done so.

You can fill out the address form directly through our
Web page at URL
http://www.bio.net/adrform.html.

The address database is reindexed nightly for WWW
access (the URL is
http://www.bio.net/).  If you are not directly on the
Internet but can
reach it by e-mail, please use our waismail server to
access the user
directory.  waismail use is described above.  You can
also request a
user address form by e-mail from
biosci-help@net.bio.net.

Please check your database entry from time-to-time to
see if your
address information is still up-to-date.  Because of
our limited
personnel resources, we ask that you resubmit a
*complete* form to
revise your entry; we only replace complete entries
and do not have
resources to edit old forms.






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From owner-recombination@net.bio.net Sun Oct 17 21:55:00 1999
Path: biosci!biosci!not-for-mail
From: Sripathi Ramadurai <sripathi@home.com>
Newsgroups: bionet.molbio.recombination
Subject: Linkage Disequilibrium
Date: 17 Oct 1999 15:55:14 -0700
Organization: @home
Lines: 21
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Approved: genestructure@yahoo.com
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Could somebody please explain to me what 'Linkage
Disequilibrium' is all
about?  All help is appreciated.

Thanks,

Sri
> 


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From owner-recombination@net.bio.net Fri Oct 22 07:28:00 1999
Path: biosci!biosci!not-for-mail
From: David Humair <david.humair@bota.unine.ch>
Newsgroups: bionet.molbio.recombination
Subject: DNA shuffling
Date: 22 Oct 1999 01:28:57 -0700
Organization: BIOSCI International Newsgroups for Molecular Biology
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Hi folks,
I want to know more about the technique of DNA
shuffling.
Do you have any indications of the technical aspects
and the reasons why
reaserchers do that...

Thank you very much

David Humair

----------
"Tell a man there are 400 billion stars and he'll
believe you;
tell him a bench has wet paint and he has to touch
it."
----------

 


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From owner-recombination@net.bio.net Tue Oct 26 09:56:00 1999
Path: biosci!biosci!not-for-mail
From: biosoftware@genamics.com
Newsgroups: bionet.molbio.recombination
Subject: Software for Science 19534
Date: 26 Oct 1999 03:56:47 -0700
Organization: SoftwareSeek
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GENAMICS SOFTWARESEEK
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http://genamics.com/software/

Genamics SoftwareSeek now indexes well over 1000
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Classifications include DNA sequence analysis,
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Linux. Over 150 online tools and resources that run
directly through your internet browser are also
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New software can be submitted on-line through our
web-site.
Marcel Dinger,
Genamics.
http://genamics.com/software/




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