HDTenEightyP/NetNews huggingface dataset:
From: deboer@bio.vu.nl (Thon de Boer)
Subject: Re: auto-mail program for BLAST?
Organization: VU Biology, Amsterdam, The Netherlands
Distribution: bionet
Date: Mon, 5 Oct 1992 13:31:58 GMT

theiss@CSHL.ORG (Bobbie Peters in Grace) writes:
: We have a program here that sends parameters & sequences to the old
: FASTA e-mail address in the correct format. It would ask the user questions -
: What is the name of the sequence, what databank do you want to search against,
: are these parameters OK, etc. Then it mailed the info to the old 
: fasta bio.net address.
: I seem to remember that someone else offered the same type of program 
: ages ago for FASTA. Rather than us re-writing the fasta program,
: has anyone written an auto mail program for BLAST?
: 
: Along the same lines, is there a list of programs like BLAST, SeqApp, etc
: that are available via e-mail? This doesn't seem to be a question that
: Archie would easily answer.
: 
There are several of those programs available for different computers.
There is GenBankSearch@NCBI for the MAC by Don Gilbert
NCBI en GRAIL shells for VMS by Foteos Macrides and
mailfasta3.0 for UNIX platforms, which I wrote.

You can find most of these programs at the iubio ftp server (fly.bio.indiana.edu)
and mailfasta3.0 can also be retrieved directly from me by ftp to bio.vu.nl /molbio
and through a gopher hole at grampus.bio.vu.nl at port 9001.

Sincerely, Thon de Boer

Here is the announcement of mailfasta3.0

*******

This is version 3.0 of the mailfasta program. It is a UNIX shell script which
will take a DNA or PROTEIN sequence and will mail it to all the
different mail-servers where it can be searched against the DNA or PROTEIN
databases using the FASTA and/or BLAST programs. It can also be used to identify
ORFs using the GRAIL and/or GeneID/NetGene mail servers and to identify homology
using PROSITE blocks with the BLOCKS server.
It uses the new BLAST server at NCBI and the FLAT server in Japan for FASTA
searches because the services at GenBank will be terminated at the end of this
month. 

It is packed as an shell archive. It contains :
mailfasta : the UNIX shell script
cid.c     : A small c program which will determine if the sequence is DNA or AA
getentry  : A shell script which can be used to retrieve entries of interest
mailfasta.doc : The documentation file

The shar file will unpack all these files and will compile cid.c into cid
using the cc c compiler.

mailfasta makes use oif the program 'readseq' for file conversion.
This program MUST be present and is NOT packed with this shar file.
It can be obtained via FTP from various FTP sites (fly.bio.indiana.edu etc.)

This shar file can also be found on this FTP site. First in the 'incomming'
directory and later in the /molbio/unix directory.
From: BIONET@FRCGM51.EARN
Newsgroups: bionet.software
Subject: Re: Biocomputing Departments
Date: 27 Sep 92 17:14:00 GMT
Distribution: bionet
X-Envelope-To: bio-software@daresbury.ac.uk
Original-To: bio-software@UK.AC.DARESBURY
X-Vms-To: IN%"bio-software@daresbury.ac.uk"


 
        Excellent idea!
        We have no "Biocomputing Department" here at the lab, just a Vax
and 2 poor guys (including me) trying to make research _and_ serve about 60
people. Certainly, this kind of situation must be very common.
        I, also, would be interested in hearing both from labs like mine
and "richer" or "luckier" ones.
        I would certainly answer Keith Ellison if he sends a questionnaire.
 
   ---------------------------------------------------------------
  | J-L. Risler                         |                         |
  | CNRS                                |  Bionet@frcgm51.bitnet  |
  | Centre de Genetique Moleculaire     |  Risler@frcgm51.bitnet  |
  | 91190 Gif sur Yvette   France       |                         |
   ---------------------------------------------------------------
From: sendall@dxpt01.cern.ch (Mike Sendall)
Newsgroups: bionet.software
Subject: Re: Archie, WAIS etc
Date: 27 Sep 92 16:58:21 GMT
Reply-To: sendall@dxcern.cern.ch
Distribution: bionet
Organization: CERN (European Laboratory for Particle Physics)


There is at least one version of the Archie database available
via WAIS - try asking the WAIS Directory of servers about archie.
From: Fergus_Doherty@vme.ccc.nottingham.ac.uk
Newsgroups: bionet.software
Subject: FASTA for the Mac?
Date: 29 Sep 92 08:57:01 GMT
Distribution: bionet
Original-To: Bio-soft@uk.ac.daresbury

Hello, I have seen mention of FASTA for the Mac, either under development, 
or perhaps ready, anyone know anything about this?  With a CD-ROM database 
this might be useful for teaching.
Fergus Doherty, Nottingham University, UK.
From: francis@monod.Biol.McGill.CA (Francis Ouellette)
Newsgroups: bionet.software
Subject: Re: blaze
Date: 3 Oct 92 20:49:57 GMT
Distribution: bionet
Organization: McGill University

Keith.A.Johnson@DARTMOUTH.EDU writes:

>I haven't been paying strict attention to some of the more recent postings on
>the database search programs and the ftp names now in use.  I was wondering
>if there is a site available for BLAZE searches as there is for the BLAST
>searches?  I have had a bad experience with a BLAST search and received more
>believable information from the BLAZE algorithm.

from "Mr net.bio.net" himself: (posted on bio-matrix just a couple of
days ago)


> kristoff@net.bio.net (David Kristofferson) writes:
> 
> >Since the end of the GenBank On-line Service, BLAZE is now only
> >available commercially from IntelliGenetics and MASPAR.
> 
> David,
> 
> where do we get info about rates and access to the "commercial" BLAZE?
> 
> thanks,
> 
> francis
> 

# You can either contact consult@presto.ig.com or call IG at
# 415-962-7300.
# 
#				Sincerely,
#
#				Dave Kristofferson
#				BIOSCI/bionet Manager
#
#				kristoff@net.bio.net


hope this helps,

francis


--
| B.F. Francis Ouellette  
| manager, yeast chromosome I project
| dept of biology, McGill university, Montreal, Qc, Canada
| francis@monod.biol.mcgill.ca
From: ahouse@hydra.rose.brandeis.edu
Newsgroups: bionet.software
Subject: GCG7 to Paup translation?
Keywords: GCG, Paup, file translation
Date: 3 Oct 92 20:58:16 GMT
Organization: Brandeis University

I need to find a program that will take me from the multiple sequence
alignments that I can get out of GCG 7's pileup program to the format required
by Paup on the Mac.

	Do you all do this by hand?  Do you have a good/better multiple
sequence alignment tool on the Mac?

	Any info would be very helpful,

	- jeremy

:::::::::::::
	Jeremy John Ahouse
	Center for Complex Systems and Biology Dept
	Brandeis University
	Waltham, MA 02254-9110

	(617) 736-4954
	email: ahouse@hydra.rose.brandeis.edu



--

	:::::::::::::::::::::::::::::::
	Jeremy Ahouse
	Center for Complex Systems
Newsgroups: bionet.software
From: R.S.Habib@lut.ac.uk (Robert Habib)
Subject: subscribe
Original-To: bio-soft@uk.ac.daresbury
Distribution: bionet
Date: Mon, 28 Sep 1992 15:29:49 GMT
X-Mailer: ELM [version 2.3 PL0 (LUT)]


I am a Ph.D student majoring biomedical engineering applications in underwater systems
I will be grateful if subscribe me to the list and advice me hoe to obtain further signal processing software releses related to biomedical applications such as ECG analysis and compression and  signal acquisition with IBM compatible 

I appreciate your advice in this matter, nd thank you





Yours sincerely



Robert Sh Habib-Istepanian
From: POSTMASTER@GUNBRF.NBRFNET.GEORGETOWN.EDU
Newsgroups: bionet.software
Subject: Re: Genbank FASTA server -> NCBI?
Date: 28 Sep 92 16:52:08 GMT
Distribution: bionet

In addition to the previously mentioned FASTA servers at
fasta@embl-heidelberg.de and flat-netserv@smlab.eg.gunma-u.ac.jp,
for more than two years the National Biomedical Research Foundation has
offered E-mail FASTA searches against the protein sequence databases for
protein and nucleotide sequences.  Nucleotide sequences are translated in six
reading frames using one of six selectable genetic codes.  In addition to the
the PIR1, PIR2, PIR3 and NRL_3D databases, since July 1992 the protein
databases searched also include the Max Planck Institute PATCHX database of
non-redundant sequences from the following sources
  MIPSOwn   (MIPS preliminary entries)
  PIRMOD    (MIPS/PIR preliminary entries)
  MIPSH     (MIPS yeast entries)
  MIPSTrn   (MIPS preliminary translations)
  EMTrans   (EMBL automatic translations)
  SwissProt (SwissProt entries)
  GenPept   (GenBank automatic translations)
  Kabat     (Kabat entries)
  PSeqIP    (NEWAT, PSD and PGTrans)
For those interested in searching only for sequences with known conformation
it is possible to select the NRL_3D database exclusively.
Instructions for using the server can be obtained by sending the commands
  HELP
and
  HELP SEARCH
to
  FILESERV@GUNBRF on BITNET
or
  FILESERV@NBRF.Georgetown.EDU on Internet.
------------------------------------------------------------------------
                                 Dr. John S. Garavelli
                                 Database Coordinator
                                 Protein Identification Resource
                                 National Biomedical Research Foundation
                                 Washington, DC  20007
                                 POSTMASTER@GUNBRF.BITNET
                                 POSTMASTER@NBRF.GEORGETOWN.EDU

Newsgroups: bionet.software
From: dan@cubmol.bio.columbia.edu (Daniel Zabetakis)
Subject: Re: Genbank FASTA server -> NCBI?
Organization: Columbia University, Dept. of Biological Sciences.
Date: Tue, 29 Sep 1992 18:02:10 GMT

In article <28SEP199211032524@seqvax.caltech.edu> mathog@seqvax.caltech.edu (David Mathog) writes:
>>
[complaint about loss of FASTA server]
>
>Ex Genbank-FASTA users need to replace this service, and soon (ie,
>TOMORROW). Speaking as a US taxpayer, I'd say that it would make a bit more
>sense for the NCBI to scrape up the money to get that FASTA server back on
>line than it does for the NIH/NSF to spend many times that amount putting
>new hardware in (50?) sites like mine!  I don't have the figures, but you
>folks have a budget of what, >1M$/year? I just do NOT believe that the NCBI
>does not have the resources to put together a FASTA server. 
>
   Hear Hear!  I wanted to say this, but didn't think I was in much of a
position to complain. But as long as others are complaining. I bet there
are _many_ people who would also make this complaint.

  DanZ

-- 
This article is for entertainment purposes only. Any facts, opinions,
narratives or ideas contained herein are not necessarily true, and do
not necessarily represent the views of any particular person.  

Newsgroups: bionet.software
From: mrl775@tigger.jvnc.net
Subject: Biocomputing Departments
Followup-To: bionet.software
Reply-To: mrl775@tigger.jvnc.net
Organization: TheNews 
Distribution: na
Date: Sun, 27 Sep 1992 03:32:00 GMT

 Hello

I have watched this group grow for a while, and have also watched the
.signatures as well.  I have begun to see quite a few with the monikers
"Biocomputing facitily" or "Molecular Biology Computing" and etc.  Has anyone
taken a poll recently to see exactly what is around for "biocomputing
facilities"?  Specifically, what services are offerred, what the staffing
levels are, how many users, etc.  I know from a personal stand point that it is
difficult to justify new staff, equipment and etc., when you can't point your
finger at some other institution and say... Geez, look what they have compared
to us, we need more staff!

So, how about the following.... Can we have an informal survey of the various
"biocomputing facilities" on the net?  Such information as the number of staff,
number of users, main responsibilities, and etc. would be great... If people
are interested, I could volunteer to collate the appropriate questions into a
questionaire, and could colate the data if such a survey becomes real.

What do you all think?

Later,

Keith Elliston
mrl775@tigger.jvnc.net
From: mangalam@SALK-SC2.SDSC.EDU
Newsgroups: bionet.software
Subject: SeqApp: changing addresses for searches, retrievals
Date: 26 Sep 92 23:11:15 GMT
Distribution: bionet

Hi
   Is there a way for end users to change the addresses in the Internet
services part of SeqApp to reflect the changes in services now taking place
as Genbank slides across country?  Or will you have to release a new
version of SeqApp with the new services entered and recompiled?
   I poked around with ResEdit and found a resource which I presumed to be
responsible for addressing, but after modifying it to use the ncbi address,
there was no change in the mail behavior.
   If this not possible in SeqApp's present form, it would be nice to see
in a later version.

Cheers,
Harry

Harry Mangalam                                   Vox:(619) 453-4100, x250
Dept of Biocomputing                                   Fax:(619) 552-1546
The Salk Institute                             mangalam@salk-sc2.sdsc.edu
10010 N Torrey Pines Rd                        mangalam@salk-sgi.sdsc.edu
La Jolla CA 92037                                    mangalam@salk.bitnet
From: NUM239@MBDS.NRC.CA
Newsgroups: bionet.software
Subject: RE: GCG7 to Paup translation? (A)
Date: 5 Oct 92 00:10:58 GMT
Distribution: bionet

Hi:
Do you know of such a program that will do the same on IBM compatibles
or on the VAX?
Newsgroups: bionet.software
Subject: Re: UNIX Scripts for NCBI Sequence Server
From: robison1@husc10.harvard.edu (Keith Robison)
Date: 6 Oct 92 14:19:34 GMT

While it is not essential, the following addition
to 'fetch' is better design:

after the line:
	echo "DATALIB " $1 >>gpf
insert the line:
	shift

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

robison@ribo.harvard.edu
From: CX13@MUSICA.MCGILL.CA ("Yannick@CX13")
Newsgroups: bionet.software
Subject: good MAC terminal emulator?
Date: 2 Oct 92 16:59:21 GMT
Distribution: bionet

Hello Netters!

Can somebody suggest a good MAC terminal emulator running under
DECNET, preferably something small to accomodate our low-grade
MAC and which will allow TEKTRONIX graphics?

In particular, is there something available in one of the FTP
sites?

Thanx,

Yannick Pouliot
Montreal Neurological Institute
Newsgroups: bionet.software
From: moboyle@lonestar.utsa.edu (Michael P. O'boyle)
Subject: CAI
Organization: University of Texas at San Antonio
Date: Mon, 28 Sep 1992 22:17:07 GMT

I am posting for someone else:

HE WRITES:

        I am investigating supplementing intoductory biology lab
with interactive video disk (Computer aided instruction - CAI)

Anybody know any existing systems or software?

Please e-mail responses to 

pf@harlan.ls.utsa.edu

Thanks,

Dr. Paul Farnsworth
From: zauhar@SHIVA.PSU.EDU (Dr. Randy Zauhar)
Newsgroups: bionet.software
Subject: Biocomputing Depts
Date: 27 Sep 92 19:51:37 GMT
Distribution: bionet


In regard to Keith Elliston's recent posting - 

  I direct the Center for Computational Biology in the Biotech. Institute
here at Penn State. Despite the "official" title, it is a one-man operation
(guess who). I serve the interests of about 100 users, while still trying
to carry out my own research projects. The facility here includes two 
SPARC stations (running Intelligenetics), and a four-processor IRIS 
(used for molecular modeling (mostly SYBYL and QUANTA), phylogenetic
analysis (PAUP, etc.), and a variety of other packages). 
My facility is perhaps unusual in that it
combines both molecular biology and molecular modeling applications.

  If you want to send a more detailed survey, I will be happy to respond.
If others in my situation wanted to form some sort of newsgroup, I would be
pleased to contribute.

   Randy J. Zauhar
   Penn State
   zauhar@shiva.psu.edu
From: spl@szechuan.ucsd.edu (Steve Lamont)
Newsgroups: bionet.software
Subject: Re: Microscope image processing (summary)
Date: 3 Oct 92 22:09:39 GMT
Organization: University of Calif., San Diego/Microscopy and Imaging Resource
NNTP-Posting-Host: szechuan.ucsd.edu

In article <199210032106.AA18766@mendel.sis.pasteur.fr> bloch@pasteur.fr (Laurent Bloch) writes:
>   After digitization, you can reconstruct the image with a program called
>SYNU (SYnthetic UNiverse) from UCSD and the San Diego Supercomputer Center
>(costs ~$100 to cover costs) which can handle huge data sets and render
>beautiful reconstructions (call David Hessler @ 619 534 7968 or Steve Young
>@ 619 534 3539 - unfortunately, it only runs on SGI hardware)

Again, a correction to this:

Please do NOT call David Hessler or Steve Young or send email to the
San Diego Supercomputer Center.  SDSC no longer distributes Synu.  If
you have any questions, please send me email (spl@szechuan.ucsd.edu)
or call Dolores Robinson at (619) 534-1392.  Since we have a small
staff, unless you have a burning question that can only be answered
over the phone, we'd appreciate sending email rather than phoning us.

For further information, please see my earlier posting containing the
Synu FAQ-List.

Thanks.

							spl
-- 
Steve Lamont, SciViGuy -- (619) 534-7968 -- spl@szechuan.ucsd.edu
UCSD Microscopy and Imaging Resource/UCSD Med School/La Jolla, CA 92093-0608
"If you don't think people are this crazy, you need to move to LA!"
                                     - Gary Stollman
From: g5000005@nickel.laurentian.ca
Newsgroups: bionet.software
Subject: Wanted: Statistica 3.1 manual
Date: 30 Sep 92 19:15:27 GMT
Organization: Laurentian University

Hello netters!

	I am looking for a manual/book for the statistical analysis program 
called Statistica 3.1 (for DOS). I am currently using VAX/VMS SPSSx but I will
be graduating soon (what time is it now?) and have to decide between SPSS-PC+ 
and Statistica for my PC.

	If anyone has used this package I would be interested to hear your 
comments/criticisms regarding this package.

	Thanks in advance!

Norm
From: ins660u@lindblat.cc.monash.edu.au (Mr Yeung Siu Kwan)
Subject: multilink wanted
Organization: Monash University
Date: Thu, 1 Oct 1992 08:20:37 GMT

	Anyone has the software -- multilink..?
    can you tell me where can I get it...
     
         thank a lot !!!!
				ALEX. 


Newsgroups: bionet.software
From: lpcasson@phoenix.Princeton.EDU (Lawrence P. Casson)
Subject: Plasmid Drawing Program
Originator: news@nimaster
Organization: Princeton University
Date: Wed, 30 Sep 1992 15:40:06 GMT


Does anyone out there know of a simple Macintosh program that will
produce a drawing of a plasmid identifying restriction enzyme sites
by enzyme name and location using just a list of restriction enzymes
with numbers (digestion sites)?  I don't need the accuracy a GCG
program, just something simple and quick.

Thanks.
From: robison1@husc10.harvard.edu (Keith Robison)
Newsgroups: bionet.software
Subject: Sequence Searching Algorithms
Date: 5 Oct 92 20:31:53 GMT

Someone posted a query recently about how to search for a
defined site (such as a restriction enzyme recognition site)
in a biological sequence, and the one reply I saw mentioned
simple scanning algorithms.  I would just like to point out
that while such algorithms are both easy to write and commonly
used (every searcher I have written has used one), a more elegant
and sometimes faster algorithm is a Finite State Machine.  In brief,
a Finite State Machine (FSM) improves on a simple scanning algorithm by
knowing when it can "skip ahead".

For example, suppose you wish to look for the site "AATTTCCC" in DNA.
Suppose a stretch of DNA contained the sequence "AATTTGG". A simple
scanner would compare (| - match, * - mismatch):

try #1          try #2          try #3

AATTTCCC	AATTTCCC	AATTTCCC
|||||*		|*		*
AATTTGG		ATTTGG		TTTGG


Now, we humans know that once #1 has failed, you can skip past the whole
AATTTGG segment because "ATTTGG" cannot overlap "AATTTCCC" in any way.
An FSM incorporates this idea, and thus can be faster.

If you can find the journal, a very good description of FSMs can be 
found in:

  Tyler, EC, MR Horton, and PR Krause.  1991.  Comp.&Biomed Res. 24:72-96.
	A review of algorithms for molecular sequence comparison.

Another relevant reference is:
   Altschul, SF, W Gish, W Miller, EW Myers, and DJ Lipman.  1990. JMB 214:1-8.
	 Basic local alignment search tool.

 as BLAST uses an FSM in the initial stages of the database search.



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

robison@ribo.harvard.edu 

P.S. Apologies for not posting this as a follow-up -- I was rushing to
     get a poster ready when the original showed up and the local
     news server has apparently "expired" it.
From: lipman@void.nlm.nih.gov (David Lipman)
Newsgroups: bionet.software
Subject: NCBI FASTA mail server
Date: 5 Oct 92 16:22:55 GMT
Organization: National Library of Medicine
X-Newsreader: Tin 1.1 PL4


 (the previous msg omitted the 1st line)

communications to NCBI, it's clear that there is definite interest in
having a NCBI FASTA mailserver.  We had initially decided to forgo this
because of the demands on resources, and because, as mentioned by M.
Cherry, we had been making BLAST available to a number of sites on an
experimental basis and had not received explicit feedback regarding the
need for additional access to FASTA.  Bill Pearson has generously
agreed to modify FASTA so that it can read the file format we use
centrally for sequence searching (this same format will be available on
CDROM's updated every 2 months starting in February).  Thanks to Bill's
work, the single format will avoid the need for another copy of all the
sequence data on our BLAST server.

When this software is available and tested we'll put the FASTA server
up for public access and announce the availability via the bulletin
boards and in the header messages of our e-mail servers.  The priority
of these searches will probably be lower than BLAST searches due to
their greater requirements for CPU cycles.

Supporting additional computational tools makes real demands on our
resources and have to be balanced by significant gains in
functionality.  For example, I'm not convinced that FASTN searches are
really worth adding -- although they result in alignments with gaps,
they are unlikely to yield matches that would not be found with
BLASTN.  In order to detect significant nucleic acid similarities in
such large databases requires fairly strong similarity (coding or
non-coding) and these non-gapped regions would be found with BLASTN.
This, of course, is arguable and your input is appreciated.

We will be doing our best to continue to upgrade the sequence searching
facilities at NCBI, incorporating new computational approaches developed
at NCBI and from researchers around the world.  Suggestions are welcome!

Thanks,
David Lipman
NCBI
From: toms@fcs260c2.ncifcrf.gov (Tom Schneider)
Newsgroups: bionet.info-theory
Subject: Re: Mead and Conway (Section 9.11)
Date: 28 Sep 92 22:56:53 GMT
Distribution: bionet
Organization: Frederick Cancer Research and Development Center

In article <9209250126.AA04548@eureka.buc.edu.au> kjm@buc.edu.au (Kevin Moore) writes:

| Entropy itself is anthropomorphic, in the sense that it depends on how much we
| know about a system. (Jaynes, in "Gibbs vs. Boltzmann entropies" American
| Journal of Physics 1965 demonstrates this rather well)

This is wrong (or "not right" for those with weak hearts... :-) - the
entropy change of a ribosome has nothing whatsoever to do with humans.
Entropy changes are only anthropomorphic when you are discussing humans!!

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
Newsgroups: bionet.info-theory